Adding as many test data files into public/testdata as possible

public/testdata/FundamentalsTest.annotated.db.subset.final.HG00625.vcf

@@ -0,0 +1,25 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Validation_Data/VariantEval/FundamentalsTest.annotated.db.subset.final.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=[HG00625] select_expressions=[] excludeNonVariants=false excludeFiltered=false"
+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=1	GT:DP:GQ:PL	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=3	GT:DP:GQ:PL	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.
+20	10019093	rs575534	A	G	69795.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	1/1:5:15:172,15,0
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=2;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DP=1;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:4:12:139,12,0

public/testdata/FundamentalsTest.annotated.db.subset.final.NA12045.vcf

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12045
+20	10003358	rs926982	A	C	92318.04	PASS	DBSNP129;DBSNP132;DP=5	GT:DP:GQ:PL	0/1:5:51:51,0,95
+20	10003692	rs2064653	A	G	119873.04	PASS	DBSNP129;DBSNP132;DP=4	GT:DP:GQ:PL	0/1:4:20:20,0,85
+20	10015679	rs113024248	C	.	2829.33	PASS	DBSNP132;DP=0;OMNI	GT:DP:PL	./.
+20	10015790	rs114356776	G	.	43.60	PASS	DBSNP132;DP=0	GT:DP:PL	./.
+20	10019093	rs575534	A	G	69795.04	PASS	DBSNP129;DBSNP132;DP=6;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
+20	10019169	rs7260784	C	.	1193.61	PASS	DBSNP129;DBSNP132;DP=6;HAPMAP;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
+20	10032432	rs78089752	A	.	367.04	PASS	DBSNP132;DP=8;OMNI	GT:DP:GQ:PL	0/0:8:24:0,24,293
+20	10037119	.	G	.	469.85	PASS	DBSNP129;DP=2	GT:DP:GQ:PL	0/0:2:6:0,6,65
+20	10047435	rs598275	G	A	82495.04	PASS	DBSNP129;DBSNP132;DP=2;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0

public/testdata/FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
+20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0

public/testdata/FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf

@@ -0,0 +1,18 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/FundamentalsTest.annotated.db.subset.final.vcf

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
+20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/FundamentalsTest.annotated.db.subset.snps_and_indels.vcf

@@ -0,0 +1,26 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	PASS	NONCPG;AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338
+20	10003358	rs926982	A	C	92318.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	FAIL	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
+20	10019093	rs575534	A	G	69795.04	PASS	NONCPG;AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
+20	10019169	rs7260784	C	.	1193.61	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	NONCPG;AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	FAIL	CPG;AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0
+20	31384616	.	A	AG	12610.94	PASS	NONCPG;AC=96;AF=0.5000;AN=192;DP=5288;Dels=0.00;HRun=2;HaplotypeScore=9.2447;MQ=61.14;MQ0=0;QD=2.38;SB=-2.03;sumGLbyD=2.39	GT:DP:GQ:PL	0/1:50:99:161,0,486	0/1:55:99:123,0,615	0/1:51:87.95:88,0,647
+20	62172300	.	CGG	C	440.96	FAIL	CPG;AC=25;AF=0.1316;AN=190;DP=2673;Dels=0.01;HRun=1;HaplotypeScore=12.2310;MQ=58.24;MQ0=0;QD=0.63;SB=-58.90;sumGLbyD=1.00	GT:DP:GQ:PL	0/0:29:45.69:0,46,1437	0/0:16:16.13:0,16,799	0/1:31:32.81:33,0,1141

public/testdata/GIH.samples.list

@@ -0,0 +1,70 @@
+NA20845
+NA20846
+NA20847
+NA20849
+NA20850
+NA20851
+NA20852
+NA20853
+NA20854
+NA20856
+NA20858
+NA20859
+NA20861
+NA20862
+NA20863
+NA20864
+NA20866
+NA20867
+NA20868
+NA20869
+NA20870
+NA20871
+NA20872
+NA20873
+NA20874
+NA20875
+NA20876
+NA20877
+NA20881
+NA20885
+NA20886
+NA20887
+NA20888
+NA20889
+NA20890
+NA20891
+NA20892
+NA20894
+NA20895
+NA20896
+NA20897
+NA20898
+NA20899
+NA20901
+NA20902
+NA20903
+NA20904
+NA20906
+NA20908
+NA20910
+NA20911
+NA21086
+NA21088
+NA21089
+NA21090
+NA21091
+NA21092
+NA21094
+NA21097
+NA21098
+NA21099
+NA21100
+NA21101
+NA21102
+NA21103
+NA21137
+NA21141
+NA21142
+NA21143
+NA21144

public/testdata/MendelianViolationEval.ped

@@ -0,0 +1,6 @@
+TRIO	TRIO_MOTHER	0	0	0	-9
+TRIO	TRIO_FATHER	0	0	1	-9
+TRIO	TRIO_CHILD	TRIO_MOTHER	TRIO_FATHER	0	-9
+PAIR	PAIR_PARENT	0	0	0	-9
+PAIR	PAIR_CHILD	PAIR_PARENT	0	1	-9
+UNRELATED	UNRELATED_INDIVIDUAL_CONTROL	0	0	0	-9

public/testdata/MendelianViolationEval.vcf

@@ -0,0 +1,22 @@
+##fileformat=VCFv4.0
+##MendelianViolationEvaluator="This file contains genotypes with mendelian violations in the input data. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_PARENT	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
+1	10109	.	A	T	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	0/0:40:0,40,200	0/1:30:30,0,200	0/0:50:0,50,200	0/1:30:30,0,200	0/0:50:0,50,200	
+1	10147	.	C	A	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
+1	10150	.	C	T	99	PASS	.	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	1/1:50:200,50,0	0/0:40:0,40,200	1/1:50:200,50,0	0/0:40:0,40,200
+1	10177	.	A	C	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	0/0:50:0,50,200	0/0:30:0,30,200	0/0:50:0,50,200
+1	10180	.	T	C	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
+1	10234	.	C	T	99	PASS	.	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/1:40:40,0,200	1/1:50:200,50,0	0/1:40:40,0,200
+1	10235	.	T	A	99	PASS	.	GT:GQ:PL	0/1:50:50,0,200	1/1:40:200,40,0	0/0:30:0,30,200	0/1:50:50,0,200	0/0:30:0,30,200	0/1:50:50,0,200
+1	10236	.	A	G	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	0/0:50:0,50,200	0/0:40:0,40,200	1/1:30:200,30,0	0/0:50:0,50,200	1/1:30:200,30,0
+1	10250	.	A	C	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	1/1:50:200,50,0	1/1:40:200,40,0
+1	10257	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/0:30:0,30,200	1/1:50:200,50,0
+1	10285	.	T	C	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	1/1:50:200,50,0	0/1:40:40,0,200	1/1:30:200,30,0	0/1:40:40,0,200	1/1:30:200,30,0
+1	10297	.	C	T	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	1/1:30:200,30,0	0/0:50:0,50,200	1/1:40:200,40,0	0/0:50:0,50,200	1/1:40:200,40,0
+1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:0:0,0,0	1/1:50:200,50,0	0/1:0:0,0,0	1/1:50:200,50,0
+1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
+1	10310	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0
+1	10315	.	C	T	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0

public/testdata/MultiSample.vcf

@@ -0,0 +1,103 @@
+##source=UnifiedGenotyper
+##format=VCRv3.2
+##reference=human_b36_both.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA11894	NA11992	NA06994	NA07037	NA12760	NA12761	NA12414	NA12762	NA12716	NA12717	NA10851	NA11919	NA11918	NA07347	NA12873	NA12874	NA06986	NA06985	NA07346	NA12763	NA11994	NA11993	NA11995	NA11840	NA12234	NA07000	NA12003	NA07357	NA11920	NA12287	NA12144	NA07051	NA12828	NA12776	NA12044	NA11831	NA11830	NA12045	NA12872	NA12489	NA11881	NA12043	NA11832	NA12751	NA12750	NA11931	NA12155	NA12154	NA12249	NA12156	NA12815	NA11829	NA12749	NA12812	NA12813	NA12814	NA12004	NA12005	NA10847	NA12006	
+1	10000005	.	A	T	0.00	.	AF=0.01;NS=60;SB=0.22	GT:RD:GQ	./.	0/0:5:3.00	0/0:2:2.11	0/0:2:2.14	./.	0/0:1:1.84	0/0:1:1.83	0/0:1:1.84	0/0:5:3.04	0/0:1:1.83	0/0:7:3.40	./.	./.	./.	0/0:1:1.84	0/0:4:2.74	0/0:6:3.34	0/0:2:1.91	0/0:3:2.43	0/0:1:1.84	0/0:1:1.84	0/0:1:1.83	./.	0/0:3:2.44	0/0:1:1.84	0/0:2:2.10	0/0:1:1.83	0/0:5:3.03	0/0:9:3.71	0/1:2:1.54	0/0:2:1.90	0/0:2:2.14	0/0:1:1.84	0/0:1:1.83	./.	0/0:6:3.27	0/0:5:2.51	0/0:4:2.49	0/0:3:2.44	0/0:2:2.06	0/0:4:2.74	0/0:1:1.84	0/0:3:2.06	0/0:1:1.83	0/0:1:1.84	./.	0/0:9:4.23	0/0:3:1.92	0/0:2:2.14	0/0:1:1.84	0/0:2:2.14	0/0:4:2.44	0/0:1:1.84	0/0:2:2.14	0/0:1:1.84	0/0:1:1.84	0/0:1:1.83	./.	0/0:1:1.84	0/0:1:1.84
+1	10000007	.	T	A	8.15	.	AF=0.01;NS=60;SB=0.21	GT:RD:GQ	./.	0/0:4:2.42	0/0:2:1.71	0/0:2:2.12	./.	0/0:1:1.82	0/0:1:1.82	0/0:2:1.73	0/0:4:2.72	0/0:1:1.82	0/0:7:3.29	./.	./.	0/0:1:1.82	0/0:1:1.82	0/0:4:2.72	0/0:4:2.72	0/0:2:2.07	0/0:2:2.12	0/0:1:1.82	./.	./.	./.	0/0:3:2.42	0/0:1:1.82	0/0:3:2.12	0/0:1:1.82	0/0:6:2.73	0/0:8:3.27	1/0:2:1.52	0/0:2:1.67	0/0:2:2.12	0/0:1:1.82	0/0:1:1.82	./.	0/0:6:3.33	0/0:4:2.72	0/0:4:2.72	0/0:3:2.42	0/0:3:2.12	0/0:4:2.72	0/0:1:1.82	0/0:2:2.12	0/0:1:1.82	0/0:1:1.82	0/0:1:1.82	0/0:8:3.93	0/0:3:2.01	0/0:2:2.12	./.	0/0:2:2.12	0/0:4:2.42	0/0:1:1.82	0/0:2:2.12	0/0:2:1.58	0/0:1:1.82	0/0:1:1.82	./.	0/0:1:1.82	0/0:1:1.82
+1	10000065	.	C	G	0.00	.	AF=0.01;NS=60;SB=2.50	GT:RD:GQ	0/0:2:2.33	0/0:8:4.13	0/0:3:2.63	0/0:5:3.23	0/0:4:2.92	0/1:3:0.82	0/0:5:3.23	0/0:3:2.63	0/0:6:3.53	0/0:2:2.33	0/0:8:4.13	0/0:1:1.91	0/0:2:2.33	0/0:2:2.33	0/0:1:2.03	0/0:6:3.53	0/0:10:4.73	0/0:2:2.33	0/0:4:2.93	0/0:2:2.33	./.	./.	0/0:6:3.53	0/0:4:2.89	0/0:1:2.03	0/0:3:2.63	0/0:5:3.23	0/0:5:3.23	0/0:8:4.13	0/0:5:3.23	0/0:13:5.33	0/0:7:3.82	0/0:1:2.03	0/0:2:2.33	0/0:1:2.03	0/0:3:2.63	0/0:5:3.23	0/0:1:2.03	0/0:3:2.63	0/0:2:2.09	0/0:3:2.63	0/0:2:2.33	0/0:3:2.63	0/0:4:2.93	0/0:2:2.33	0/0:4:2.93	./.	0/0:2:2.32	0/0:3:2.63	0/0:4:2.93	0/0:4:2.93	0/0:3:2.62	0/0:2:2.32	0/0:4:2.93	0/0:2:2.33	0/0:1:2.03	./.	0/0:2:2.33	0/0:1:2.03	0/0:6:3.53
+1	10000074	.	T	C	2.32	.	AF=0.01;NS=60;SB=-0.24	GT:RD:GQ	0/0:2:2.42	0/0:8:4.22	0/0:2:2.19	0/0:6:3.62	0/0:3:2.72	0/0:4:2.90	0/0:5:3.32	0/0:3:2.72	0/0:6:3.37	0/0:4:3.01	0/0:9:4.22	0/0:1:2.12	1/0:2:0.38	0/0:2:2.42	0/0:1:2.12	0/0:6:3.62	0/0:12:3.77	0/0:1:2.12	0/0:4:3.02	0/0:2:2.39	0/0:1:2.12	0/0:2:2.19	0/0:5:3.29	0/0:4:3.00	0/0:1:2.12	0/0:4:2.98	0/0:4:3.02	0/0:7:3.92	0/0:10:4.65	0/0:5:2.43	0/0:7:3.92	0/0:7:3.92	./.	0/0:1:2.12	./.	0/0:3:2.71	0/0:5:3.32	0/0:1:2.12	0/0:3:2.72	0/0:2:2.42	0/0:3:2.72	0/0:3:2.72	0/0:1:2.09	0/0:4:3.00	0/0:2:2.42	0/0:4:3.02	./.	0/0:1:2.12	0/0:1:2.12	0/0:5:3.09	0/0:3:2.72	0/0:1:2.12	0/0:4:2.72	0/0:4:3.02	0/0:1:2.06	0/0:1:2.12	0/0:1:2.12	0/0:2:2.42	0/0:1:2.12	0/0:5:3.32
+1	10000078	.	G	C	0.00	.	AF=0.01;NS=60;SB=2.32	GT:RD:GQ	0/0:2:2.28	0/0:8:3.79	0/0:1:1.98	0/0:6:3.49	0/0:3:2.58	0/0:4:2.87	0/0:5:3.18	0/0:3:2.28	0/0:6:3.48	0/0:4:2.87	0/0:7:3.39	0/0:1:1.98	0/0:2:2.28	0/0:2:2.28	0/0:1:1.98	0/0:6:3.49	0/0:11:4.99	0/0:1:1.98	0/0:4:2.88	0/0:2:2.28	0/0:1:1.98	1/0:2:1.11	0/0:5:3.18	0/0:4:2.85	0/0:1:1.98	0/0:4:2.88	0/0:4:2.88	0/0:7:3.79	0/0:9:3.78	0/0:5:3.18	0/0:5:2.88	0/0:5:3.18	./.	0/0:1:1.98	./.	0/0:3:2.57	0/0:5:3.18	0/0:1:1.98	0/0:3:2.58	0/0:2:2.28	0/0:3:2.58	0/0:3:2.58	0/0:1:1.98	0/0:4:2.88	0/0:2:2.27	0/0:4:2.88	./.	0/0:1:1.68	0/0:2:2.28	0/0:4:2.39	0/0:3:2.58	0/0:1:1.98	0/0:2:2.27	0/0:4:2.88	0/0:1:1.98	0/0:1:1.98	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:7:3.66
+1	10000080	.	C	T	20.08	.	AF=0.02;NS=60;SB=-1.74	GT:RD:GQ	0/0:2:1.92	0/0:8:3.58	0/0:1:1.62	0/0:6:3.12	0/0:2:1.90	0/0:4:2.52	0/0:4:2.52	0/0:2:1.92	0/0:5:2.76	0/0:4:2.48	0/0:8:3.69	0/0:1:1.62	0/0:2:1.92	0/0:2:1.31	0/0:1:1.62	0/0:6:3.12	0/0:11:4.62	0/0:1:1.62	0/0:4:2.51	0/0:2:1.91	0/0:1:1.62	0/0:2:1.92	0/0:5:2.39	0/0:4:2.46	0/0:1:1.62	0/0:4:2.52	0/0:4:1.99	0/0:6:3.12	0/1:7:4.36	0/0:5:2.81	0/0:4:2.22	0/0:5:2.33	./.	0/0:1:1.62	./.	0/0:3:2.16	0/0:5:2.81	0/0:1:1.62	0/0:3:2.22	0/0:2:1.92	0/0:3:2.21	0/0:3:2.22	0/0:1:1.54	0/0:4:2.49	./.	0/0:3:2.22	./.	./.	0/1:2:2.04	0/0:4:2.52	0/0:3:2.22	0/0:1:1.62	0/0:2:1.92	0/0:4:2.52	0/0:1:1.62	0/0:1:1.62	0/0:1:1.62	0/0:2:1.92	./.	0/0:7:3.41
+1	10000092	.	G	A	0.00	.	AF=0.01;NS=60;SB=2.81	GT:RD:GQ	0/0:2:2.21	0/0:5:2.98	./.	0/0:8:4.00	./.	0/0:4:2.81	0/0:1:1.91	0/0:2:2.10	0/0:3:2.51	0/0:5:2.50	0/0:3:2.49	0/0:1:1.90	0/0:2:2.20	0/0:1:1.87	0/0:1:1.91	0/0:4:2.81	0/0:7:0.51	0/0:1:1.61	0/0:1:1.91	0/0:1:1.90	0/0:1:1.91	0/0:2:2.21	0/0:1:1.91	0/0:2:2.21	0/0:1:1.91	0/0:3:1.61	0/0:2:2.21	0/0:5:2.80	0/0:4:2.38	0/0:5:3.11	0/0:3:2.51	0/0:4:2.81	./.	0/0:1:1.91	0/0:2:2.21	0/0:2:2.20	0/0:3:2.51	0/0:1:1.91	0/0:3:2.51	0/0:2:2.21	0/0:4:2.81	0/0:3:2.51	./.	0/0:6:3.41	./.	0/0:3:2.51	./.	0/0:1:1.91	0/0:4:2.80	0/0:3:2.51	0/0:3:2.50	0/0:3:2.51	0/0:2:2.21	0/0:4:2.81	0/0:2:2.21	0/0:2:2.21	0/0:1:1.91	0/0:1:1.91	./.	1/0:5:0.44
+1	10000102	.	A	G	0.00	.	AF=0.01;NS=60;SB=2.66	GT:RD:GQ	0/0:1:1.98	0/0:2:1.97	./.	0/0:7:3.78	./.	0/0:5:3.18	0/0:1:1.97	./.	0/0:1:1.98	0/0:4:2.65	0/0:4:2.88	0/0:2:2.28	0/0:2:2.28	0/0:1:1.98	0/0:1:1.98	0/0:4:2.88	0/0:4:2.74	0/0:1:1.98	./.	./.	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:6:3.48	0/0:3:1.98	0/0:4:2.88	0/0:5:3.18	0/0:3:2.58	./.	./.	0/0:3:2.58	0/0:1:1.97	0/0:2:2.28	0/0:2:2.28	0/0:3:2.58	0/0:1:1.98	0/0:6:3.18	0/0:4:2.88	0/0:1:1.98	0/0:5:3.18	./.	0/0:2:2.28	0/0:2:2.28	0/0:1:1.98	0/0:4:2.88	0/0:2:2.27	0/0:3:2.58	0/0:2:2.28	0/0:1:1.98	0/0:5:3.18	0/0:2:2.28	0/0:2:2.28	0/0:2:2.28	0/1:1:0.62	0/0:1:1.98	0/0:4:2.88
+1	10000110	.	G	C	0.00	.	AF=0.02;NS=60;SB=2.88	GT:RD:GQ	0/0:1:1.81	0/0:3:2.41	0/0:1:1.81	0/0:8:3.92	./.	0/0:7:3.62	0/0:1:1.81	./.	0/0:1:1.81	0/0:1:1.81	0/0:8:3.86	0/0:2:2.11	0/0:1:1.81	0/0:2:2.11	0/0:1:1.81	0/0:4:2.71	0/0:6:3.31	0/0:1:1.81	0/0:1:1.70	0/0:2:2.10	0/0:1:1.81	0/0:1:1.81	0/0:1:1.81	0/0:2:2.11	0/0:1:1.81	0/0:4:2.11	0/0:1:1.81	1/0:5:0.30	0/0:4:2.41	0/0:4:2.71	0/0:8:3.62	0/0:2:2.11	./.	./.	0/0:2:2.11	0/0:1:1.81	1/0:3:0.12	0/0:2:2.11	0/0:3:2.41	./.	0/0:8:3.92	0/0:4:2.71	0/0:1:1.81	0/0:7:3.62	0/0:1:1.81	0/0:1:1.81	0/0:2:2.11	0/0:2:1.81	0/0:3:2.41	./.	0/0:3:2.41	0/0:1:1.79	0/0:1:1.81	0/0:5:3.01	0/0:1:1.81	0/0:2:2.11	0/0:1:1.81	0/0:1:1.81	0/0:3:2.41	0/0:4:2.71
+1	10000112	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.37	GT:RD:GQ	0/0:1:1.94	1/0:2:1.09	0/0:2:2.24	0/0:8:4.04	./.	0/0:7:3.74	0/0:1:1.94	./.	0/0:3:2.54	0/0:1:1.94	0/0:8:4.01	0/0:2:2.24	0/0:2:2.24	0/0:2:2.24	0/0:2:2.24	0/0:4:2.84	0/0:6:3.43	0/0:1:1.94	0/0:1:1.82	0/0:2:2.23	0/0:1:1.94	0/0:1:1.94	0/0:1:1.94	0/0:2:2.24	0/0:1:1.94	0/0:4:2.84	0/0:1:1.94	0/0:5:2.83	0/0:5:2.84	0/0:5:3.14	0/0:7:3.74	0/0:1:1.94	./.	./.	0/0:2:2.24	0/0:2:2.24	0/0:4:2.84	0/0:2:2.24	0/0:3:2.54	0/0:1:1.64	0/0:8:4.04	0/0:4:2.84	0/0:1:1.94	0/0:7:3.23	0/0:2:2.24	0/0:1:1.94	0/0:3:2.53	0/0:2:2.24	0/0:4:2.84	./.	0/0:3:2.54	0/0:1:1.82	0/0:2:2.23	0/0:5:3.14	0/0:1:1.64	0/0:2:2.24	0/0:2:2.24	0/0:1:1.93	0/0:3:2.54	0/0:4:2.84
+1	10000118	.	G	A	1.11	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:2:2.50	0/0:5:3.05	0/0:2:2.50	0/0:7:3.99	./.	0/0:6:3.71	0/0:3:2.80	0/0:1:1.90	0/0:5:3.41	0/0:2:2.50	0/0:8:4.22	0/0:3:2.80	0/0:2:2.50	0/0:3:2.80	0/0:2:2.49	0/0:4:3.10	0/0:7:2.88	./.	0/0:2:1.61	0/0:4:3.10	0/0:1:2.20	0/0:2:2.50	./.	0/0:1:2.20	0/0:1:2.20	0/0:3:2.50	0/0:1:2.20	0/0:4:3.11	0/0:9:4.61	0/0:5:3.39	0/0:5:3.41	0/0:2:2.50	0/0:1:2.20	0/0:1:2.20	0/0:1:2.20	0/0:3:2.80	0/0:5:3.41	0/0:2:2.41	0/0:3:2.81	0/0:1:2.20	0/0:8:4.31	0/0:6:3.71	0/0:1:2.20	0/0:8:4.30	1/0:2:0.06	0/0:1:2.20	0/0:3:2.78	0/0:2:2.50	0/0:4:3.10	0/0:1:1.90	0/0:3:2.80	0/0:1:2.18	0/0:3:2.80	0/0:5:3.41	./.	0/0:2:2.50	0/0:2:2.50	./.	0/0:3:2.80	0/0:3:2.81
+1	10000119	.	T	A	1.37	.	AF=0.01;NS=60;SB=-0.14	GT:RD:GQ	0/0:2:2.48	1/0:5:0.14	0/0:3:2.47	0/0:6:3.66	./.	0/0:6:3.67	0/0:4:2.90	0/0:1:2.18	0/0:5:3.37	0/0:2:2.26	0/0:8:3.88	0/0:3:2.77	0/0:2:2.36	0/0:3:2.78	0/0:2:2.48	0/0:4:3.08	0/0:9:3.93	./.	0/0:2:2.45	0/0:4:3.07	./.	0/0:2:2.48	./.	0/0:1:2.18	0/0:1:2.18	0/0:3:2.48	0/0:2:2.48	0/0:5:2.10	0/0:9:4.57	0/0:5:3.38	0/0:7:3.38	0/0:2:2.48	0/0:1:2.18	0/0:1:2.18	./.	0/0:3:2.77	0/0:5:3.38	0/0:3:2.76	0/0:3:2.78	0/0:1:2.18	0/0:8:4.28	0/0:6:3.50	0/0:1:2.18	0/0:8:2.57	0/0:3:2.76	0/0:1:2.18	0/0:3:2.78	0/0:2:2.47	0/0:5:3.38	0/0:1:2.18	0/0:3:2.78	0/0:1:2.18	0/0:3:2.78	0/0:5:3.38	./.	0/0:2:2.48	0/0:2:2.48	./.	0/0:3:2.78	0/0:3:2.78
+1	10000171	.	C	G	1.67	.	AF=0.01;NS=60;SB=-0.17	GT:RD:GQ	0/0:3:2.59	0/0:4:3.11	0/0:3:2.81	0/0:2:2.51	./.	0/0:4:3.11	0/0:10:4.32	0/0:3:2.81	0/0:4:3.11	0/0:5:3.42	0/0:11:5.22	0/0:5:3.41	0/0:1:2.21	0/0:3:2.81	0/0:5:3.42	0/0:2:2.51	0/0:10:4.92	0/0:2:2.51	0/0:1:2.21	0/0:3:2.81	0/0:2:2.51	0/0:5:3.11	0/0:2:2.51	0/0:2:2.51	0/0:1:2.21	0/0:10:4.92	0/0:4:3.11	0/0:2:2.51	0/0:10:4.18	0/0:4:3.12	0/0:7:4.02	0/0:8:4.32	0/0:3:2.81	./.	0/0:5:3.42	0/0:4:2.81	0/0:4:3.06	0/0:3:2.81	0/0:3:2.81	0/0:6:3.70	0/0:6:3.72	0/0:3:2.81	0/0:8:4.32	0/0:5:3.42	0/0:4:3.11	0/0:2:2.51	0/0:5:3.42	0/0:5:3.42	0/0:4:3.11	0/0:6:3.72	0/0:2:2.51	0/0:1:2.21	0/0:6:3.72	0/0:4:3.11	./.	0/0:4:3.11	0/0:3:2.81	0/1:5:0.23	0/0:1:2.21	0/0:6:3.41
+1	10000179	.	C	A	4.61	.	AF=0.01;NS=60;SB=-0.47	GT:RD:GQ	0/0:3:2.66	0/0:5:3.28	0/0:4:2.95	0/0:2:2.38	./.	0/0:3:2.68	0/0:9:4.47	0/0:4:2.68	0/0:6:3.58	0/0:4:2.98	0/0:14:5.99	0/0:3:2.68	0/0:1:2.08	0/0:4:2.97	0/0:5:3.28	0/0:3:2.68	0/0:4:2.96	0/0:1:2.08	0/0:1:2.07	0/0:3:2.66	0/0:3:2.68	0/0:6:3.55	0/0:4:2.98	0/0:3:2.68	0/0:1:2.08	0/0:10:4.17	0/0:4:2.98	0/0:2:2.38	0/0:15:6.28	0/0:5:3.28	0/0:7:3.58	0/0:9:4.43	0/0:3:2.67	1/0:2:0.76	0/0:5:3.25	0/0:6:3.58	0/0:2:2.38	0/0:4:2.97	0/0:3:2.68	0/0:4:2.98	0/0:5:3.28	0/0:3:2.68	0/0:9:4.47	0/0:4:2.98	0/0:5:3.28	0/0:2:2.38	0/0:3:2.68	0/0:5:3.13	0/0:5:3.28	0/0:10:4.78	0/0:2:2.38	0/0:2:2.38	0/0:5:3.28	0/0:4:2.98	./.	0/0:4:2.98	0/0:2:2.38	0/0:5:3.27	0/0:1:2.08	0/0:3:2.68
+1	10000190	.	G	A	4.01	.	AF=0.01;NS=60;SB=-0.41	GT:RD:GQ	0/0:3:2.69	0/0:7:3.85	0/0:6:3.60	0/0:4:2.25	0/0:1:2.09	1/0:4:0.67	0/0:9:4.22	0/0:5:3.30	0/0:7:3.90	0/0:3:2.69	0/0:13:4.56	0/0:2:2.39	0/0:1:2.09	0/0:4:2.99	0/0:5:3.29	0/0:3:2.69	0/0:7:3.09	0/0:1:2.01	0/0:1:2.09	0/0:3:2.68	0/0:2:2.39	0/0:5:2.99	0/0:2:2.39	0/0:2:2.39	0/0:1:2.09	0/0:7:3.90	0/0:5:3.27	0/0:5:3.29	0/0:11:4.80	0/0:5:3.30	0/0:10:4.80	0/0:8:4.19	0/0:2:2.39	0/0:3:2.69	0/0:6:3.58	0/0:7:3.88	0/0:3:2.69	0/0:3:2.68	0/0:4:3.00	0/0:3:2.69	0/0:5:3.30	0/0:4:2.99	0/0:6:3.58	0/0:4:3.00	0/0:4:3.00	0/0:1:2.09	0/0:2:2.39	0/0:4:2.68	0/0:6:3.59	0/0:9:4.20	0/0:2:2.39	0/0:3:2.69	0/0:2:2.09	0/0:4:2.99	./.	0/0:5:3.29	0/0:4:3.00	0/0:4:2.99	0/0:4:2.92	0/0:5:3.29
+1	10000236	.	C	T	3.91	.	AF=0.01;NS=60;SB=-0.40	GT:RD:GQ	0/0:7:3.90	0/0:5:3.27	0/0:9:4.49	0/0:10:4.80	0/0:2:2.39	0/0:2:2.40	0/0:5:3.30	0/0:4:3.00	0/0:5:3.29	0/0:5:3.28	0/0:13:5.39	0/0:2:2.40	0/0:3:1.66	0/0:3:2.70	0/0:5:3.30	0/0:2:2.40	0/0:12:5.40	0/0:2:2.40	0/0:4:2.98	0/0:3:2.68	0/0:1:2.09	0/0:1:2.09	0/0:7:3.90	0/0:2:2.39	0/0:1:2.09	0/0:4:3.00	0/0:9:4.49	0/0:4:2.70	0/0:14:5.67	0/0:2:2.39	0/0:14:5.41	0/0:7:3.48	0/0:2:2.40	0/0:4:2.99	0/0:5:3.30	0/0:6:3.55	0/0:7:3.90	0/1:2:0.66	0/0:5:3.30	0/0:7:3.90	0/0:7:3.89	0/0:6:3.60	0/0:4:2.83	0/0:2:2.40	0/0:5:3.30	0/0:2:2.40	./.	0/0:4:2.85	0/0:4:3.00	0/0:4:2.99	0/0:1:1.79	0/0:5:2.40	0/0:8:3.80	0/0:5:3.30	0/0:7:3.87	0/0:6:3.60	0/0:9:3.35	0/0:6:3.60	0/0:5:3.30	0/0:3:2.70
+1	10000256	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.27	GT:RD:GQ	0/0:3:2.65	0/0:7:3.85	0/0:5:3.10	0/0:10:4.76	./.	0/0:4:2.96	0/0:4:2.96	0/0:3:2.65	0/0:4:2.92	0/0:7:3.86	0/0:17:6.55	0/0:5:3.26	0/0:2:2.23	0/0:4:2.96	0/0:3:2.66	0/0:3:2.66	0/0:8:4.16	0/0:2:2.36	0/0:4:2.96	0/0:1:2.06	0/0:3:2.66	0/0:5:3.26	0/0:7:3.75	0/0:2:2.34	0/0:1:2.06	0/0:9:4.16	0/0:4:2.96	0/0:7:3.86	0/0:14:5.97	0/0:6:3.56	0/0:11:4.58	0/0:8:4.16	0/0:3:2.66	0/0:5:3.26	0/0:7:3.86	0/0:4:2.96	0/0:6:3.18	0/0:1:2.06	0/0:5:3.26	0/0:7:3.86	0/0:6:3.56	0/0:7:3.86	0/0:11:5.07	0/0:4:2.96	0/0:1:2.06	0/0:4:2.96	0/0:1:2.06	0/0:7:3.86	0/0:5:3.26	0/0:3:2.66	0/0:2:2.36	0/0:8:4.16	0/0:7:3.73	0/0:5:3.26	0/1:2:1.10	0/0:6:3.56	0/0:4:2.96	0/0:4:2.96	0/0:2:2.36	0/0:7:3.86
+1	10000272	.	G	A	4.68	.	AF=0.01;NS=60;SB=-0.48	GT:RD:GQ	0/0:2:2.39	0/0:11:5.09	0/0:9:4.50	0/0:7:3.90	0/0:2:2.25	0/0:7:3.90	0/0:4:2.99	0/0:3:2.69	1/0:4:0.77	0/0:6:3.57	0/0:21:8.10	0/0:5:3.28	0/0:2:2.39	0/0:6:3.60	0/0:4:2.99	0/0:4:2.99	0/0:9:4.50	./.	0/0:4:2.97	0/0:3:2.66	0/0:1:2.09	0/0:10:4.79	0/0:6:3.60	0/0:8:4.18	0/0:1:2.09	0/0:6:3.59	0/0:6:2.25	0/0:6:3.60	0/0:15:6.00	0/0:6:3.57	0/0:11:4.56	0/0:12:5.37	0/0:4:2.99	0/0:2:2.39	0/0:11:4.50	0/0:3:2.68	0/0:5:2.79	0/0:2:2.39	0/0:4:2.99	0/0:4:2.99	0/0:6:3.60	0/0:3:2.69	0/0:13:3.44	0/0:6:3.60	0/0:4:2.97	0/0:6:3.60	0/0:3:2.69	0/0:7:3.88	0/0:5:3.30	0/0:4:2.25	0/0:1:2.09	0/0:11:4.88	0/0:6:3.59	0/0:4:2.99	0/0:9:4.49	0/0:5:3.29	0/0:3:2.69	0/0:5:3.28	0/0:1:2.09	0/0:6:3.59
+1	10000281	.	T	C	1.03	.	AF=0.00;NS=60;SB=-0.11	GT:RD:GQ	0/0:3:2.95	0/0:14:5.94	0/0:6:3.55	0/0:6:3.85	0/0:3:2.93	0/0:8:4.45	0/0:5:3.25	0/0:3:2.95	0/0:5:3.55	0/0:6:3.85	0/0:17:7.14	0/0:5:3.53	1/0:3:0.02	0/0:3:2.95	0/0:4:3.25	0/0:5:3.55	0/0:11:5.35	./.	0/0:4:3.24	0/0:3:2.94	0/0:2:2.50	0/0:9:4.75	0/0:7:4.15	0/0:7:3.85	0/0:1:2.34	0/0:4:3.05	0/0:9:4.48	0/0:8:4.44	0/0:14:5.65	0/0:7:4.13	0/0:10:5.05	0/0:11:5.35	0/0:3:2.95	0/0:1:2.33	0/0:9:4.75	0/0:4:3.24	0/0:3:2.94	0/0:2:2.65	0/0:4:3.25	0/0:5:3.18	0/0:4:3.25	./.	0/0:6:3.85	0/0:7:4.15	0/0:3:2.94	0/0:5:3.55	0/0:5:3.55	0/0:7:3.85	0/0:8:4.45	0/0:4:2.88	0/0:2:2.65	0/0:8:3.77	0/0:6:3.74	0/0:4:3.25	0/0:10:5.05	0/0:6:3.85	0/0:2:2.65	0/0:7:4.15	0/0:2:2.63	0/0:7:3.85
+1	10000304	.	A	T	6.19	.	AF=0.01;NS=60;SB=-0.63	GT:RD:GQ	0/0:8:4.14	0/0:13:5.68	0/0:7:3.87	0/0:3:2.67	0/0:1:1.77	0/0:10:4.76	0/0:9:4.46	0/0:1:2.07	0/0:7:3.88	0/0:7:3.88	0/0:9:4.25	0/0:4:2.97	0/0:2:2.37	0/0:2:2.37	0/0:5:3.27	0/0:5:3.28	0/0:20:7.08	0/0:3:2.63	0/0:5:3.28	0/0:4:2.97	0/0:5:3.28	0/0:5:3.28	0/0:9:4.47	0/0:5:3.28	./.	0/0:2:2.37	0/0:12:5.38	0/0:8:3.58	0/0:16:5.38	0/0:2:2.37	0/0:10:4.48	0/0:12:5.37	0/0:3:2.67	0/0:2:2.37	0/0:7:3.87	0/0:6:3.56	0/0:3:2.67	0/0:3:2.64	0/0:3:2.67	0/0:3:2.67	0/0:3:2.67	0/0:2:2.37	0/0:7:3.88	0/0:9:4.48	0/0:8:4.14	0/0:6:3.58	0/0:6:3.58	0/0:7:3.87	0/0:6:3.58	0/0:5:2.97	0/0:3:2.67	0/0:4:2.97	0/0:7:3.88	0/0:5:3.28	0/1:2:0.97	0/0:5:3.28	0/0:2:2.37	0/0:2:2.37	0/0:2:2.37	0/0:6:3.28
+1	10000390	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.53	GT:RD:GQ	0/0:2:2.12	0/0:10:4.52	0/0:12:4.82	0/0:10:4.53	0/0:5:2.72	0/0:6:3.32	0/0:10:4.53	0/0:1:1.82	0/0:8:3.91	0/0:7:3.63	0/0:14:5.67	0/0:3:1.53	1/0:4:0.47	./.	0/0:3:2.42	0/0:4:2.72	0/0:16:5.73	0/0:2:2.12	0/0:3:2.36	0/0:3:2.42	0/0:1:1.82	0/0:6:3.32	0/0:10:4.52	0/0:4:2.42	0/0:2:2.12	0/0:9:3.93	0/0:11:4.83	0/0:7:3.31	0/0:19:6.32	0/0:5:3.02	0/0:11:4.49	0/0:9:4.23	0/0:2:2.12	0/0:3:2.42	0/0:8:3.90	0/0:6:3.32	0/0:5:2.28	0/0:4:2.72	0/0:3:2.42	0/0:6:3.32	0/0:4:2.72	0/0:4:2.72	0/0:5:3.00	0/0:4:2.72	0/0:6:3.32	0/0:5:3.02	./.	0/0:5:2.79	0/0:6:3.32	0/0:5:2.78	1/0:3:0.72	0/0:3:2.42	0/0:6:3.32	0/0:4:2.72	0/0:6:3.32	0/0:6:3.32	0/0:8:3.93	0/0:7:3.32	0/0:5:3.02	0/0:9:3.63
+1	10000517	.	G	T	1.40	.	AF=0.01;NS=60;SB=-0.15	GT:RD:GQ	0/0:3:2.88	0/0:14:5.56	0/0:15:5.80	0/0:11:5.28	0/0:4:2.88	0/0:13:5.88	0/0:9:4.38	./.	0/0:6:3.78	0/0:8:4.36	0/0:20:7.69	./.	0/0:2:2.57	0/0:5:3.48	0/0:6:3.78	0/0:2:2.57	0/0:12:5.58	0/0:6:3.75	0/0:1:2.27	0/0:11:5.28	0/0:5:3.48	0/0:4:3.17	0/0:9:3.78	0/0:8:4.38	0/0:2:2.58	0/0:8:4.31	0/0:9:4.22	0/0:9:3.98	0/0:26:9.75	0/0:9:4.68	0/0:11:4.36	0/0:9:4.67	0/0:2:2.57	0/0:2:2.57	0/0:7:3.98	0/0:5:3.48	0/0:6:3.44	0/0:1:2.27	0/0:3:2.88	0/0:6:3.78	0/0:3:2.88	0/1:4:0.16	0/0:6:3.72	0/0:5:3.48	0/0:6:3.78	0/0:6:3.78	0/0:2:2.57	0/0:8:4.38	0/0:4:3.18	0/0:11:5.28	0/0:3:2.88	0/0:4:3.18	0/0:9:4.38	0/0:3:2.88	0/0:9:4.38	0/0:5:3.48	0/0:4:3.18	0/0:8:3.89	0/0:5:3.48	0/0:8:4.08
+1	10000567	.	C	A	1.19	.	AF=0.00;NS=60;SB=-2.36	GT:RD:GQ	0/0:5:3.51	0/0:7:3.75	0/0:5:3.21	0/0:7:4.10	0/0:2:2.61	0/0:5:3.51	0/0:8:4.11	0/0:2:2.59	0/0:7:4.11	0/0:4:3.20	0/0:9:4.42	0/0:5:3.49	0/0:3:2.91	0/0:6:3.78	0/0:11:5.32	0/0:3:2.91	0/0:7:3.51	0/0:1:2.31	0/0:1:2.31	0/0:4:3.19	0/0:3:2.91	0/0:5:3.51	0/0:7:4.05	0/0:7:4.12	0/0:4:3.22	0/0:8:4.41	0/0:8:4.34	0/0:4:3.21	0/0:5:3.22	0/0:3:2.91	0/0:7:3.78	0/0:8:2.55	0/0:3:2.91	0/0:1:2.31	0/0:3:2.87	0/0:6:3.81	0/0:3:2.86	0/0:2:2.59	0/0:4:3.21	0/0:5:3.51	0/0:1:2.31	1/0:4:0.03	0/0:3:2.91	0/0:8:4.35	0/0:7:3.62	0/0:9:4.68	0/0:3:2.15	0/0:1:2.31	0/0:2:2.61	0/0:6:3.50	0/0:2:2.61	0/0:1:2.31	0/0:5:3.51	0/0:3:2.91	0/0:8:4.40	0/0:6:3.82	0/0:3:0.52	0/0:5:3.48	0/0:6:3.78	0/0:4:3.21
+1	10000602	.	C	A	2.70	.	AF=0.01;NS=60;SB=-0.28	GT:RD:GQ	0/0:3:2.74	0/0:5:3.30	0/0:4:2.28	0/0:5:3.34	0/0:1:1.84	0/0:3:2.74	0/0:7:3.94	0/0:1:2.14	0/0:11:5.14	0/0:7:3.18	0/0:7:3.93	0/0:3:2.59	0/0:5:3.33	0/0:6:3.15	0/0:12:5.45	0/0:5:3.34	0/0:5:3.20	1/0:4:0.46	0/0:1:2.14	0/0:8:4.22	0/0:2:2.44	0/0:4:3.04	0/0:5:3.28	0/0:2:2.44	0/0:4:3.04	0/0:2:2.44	0/0:9:4.19	0/0:4:3.02	0/0:6:3.64	0/0:7:3.90	0/0:2:2.44	0/0:9:4.54	0/0:3:2.74	0/0:1:2.14	0/0:2:1.75	0/0:2:2.43	0/0:3:2.74	0/0:3:2.74	0/0:4:3.04	0/0:6:3.64	0/0:6:3.64	0/0:3:2.74	0/0:1:2.14	0/0:4:3.03	0/0:6:3.59	0/0:7:3.94	0/0:4:3.04	0/0:2:2.44	0/0:3:2.74	0/0:3:2.74	0/0:4:3.04	0/0:2:2.42	0/0:7:3.65	0/0:5:3.34	0/0:1:2.14	0/0:8:4.24	0/0:5:3.31	0/0:2:2.44	0/0:4:3.04	0/0:4:2.98
+1	10000635	.	C	G	0.00	.	AF=0.01;NS=60;SB=2.42	GT:RD:GQ	0/0:6:3.49	0/0:1:1.98	0/0:5:3.16	0/0:4:2.89	./.	0/0:3:2.58	0/0:5:3.19	0/0:1:1.78	0/0:5:3.18	0/0:3:2.57	0/0:7:3.79	0/0:2:2.28	0/0:1:1.98	0/0:3:2.58	0/0:11:4.99	0/0:5:3.19	0/1:2:0.96	./.	0/0:2:2.28	0/0:5:3.18	0/0:1:1.98	0/0:1:1.98	0/0:1:1.98	0/0:4:2.89	0/0:4:2.89	0/0:3:2.57	0/0:6:3.48	0/0:4:2.89	0/0:4:2.66	0/0:2:2.28	0/0:3:2.58	0/0:9:4.39	./.	0/0:1:1.98	./.	./.	0/0:1:1.98	0/0:3:2.58	0/0:4:2.89	0/0:2:2.28	0/0:1:1.98	0/0:2:2.28	./.	0/0:2:2.28	0/0:4:2.89	0/0:6:3.49	0/0:4:2.89	0/0:1:1.98	0/0:2:2.28	0/0:2:2.28	0/0:6:3.49	0/0:2:2.28	0/0:4:2.28	0/0:5:3.19	0/0:5:3.19	0/0:7:3.79	0/0:1:1.98	0/0:4:2.88	0/0:4:2.89	0/0:1:1.98
+1	10000654	.	G	A	2.72	.	AF=0.01;NS=60;SB=-0.28	GT:RD:GQ	0/0:7:3.89	0/0:8:4.15	0/0:3:2.69	0/0:2:2.39	./.	0/0:4:2.98	0/0:7:3.88	./.	0/0:3:2.69	0/0:5:3.28	0/0:7:3.87	0/0:2:2.09	./.	0/0:6:3.57	0/0:12:5.39	0/0:4:2.99	0/0:3:2.69	0/0:1:2.03	0/0:2:2.39	0/0:8:4.12	0/0:1:2.08	./.	0/0:1:2.09	0/0:3:2.69	0/0:4:2.99	0/0:3:2.39	0/0:5:2.99	0/0:3:2.69	0/0:4:2.68	0/0:4:2.99	0/0:7:3.58	0/0:9:4.41	0/0:2:2.38	0/0:1:2.09	./.	0/0:2:2.38	0/0:2:2.39	0/0:3:2.68	0/0:4:2.99	0/0:2:2.39	0/0:2:2.39	0/0:3:2.69	1/0:1:0.46	0/0:2:2.39	0/0:6:3.59	0/0:3:2.69	0/0:4:2.97	0/0:3:2.69	0/0:2:2.39	0/0:3:2.69	0/0:7:3.89	0/0:2:2.39	0/0:2:2.39	0/0:4:2.99	0/0:2:2.39	0/0:6:3.59	0/0:2:2.38	./.	0/0:4:2.60	0/0:3:2.69
+1	10000665	.	A	G	0.00	.	AF=0.01;NS=60;SB=2.48	GT:RD:GQ	0/0:6:3.55	0/0:8:4.14	0/0:3:2.34	0/1:2:0.82	./.	0/0:4:2.95	0/0:8:4.15	./.	0/0:4:2.95	0/0:6:3.55	0/0:5:3.25	0/0:2:2.34	0/0:1:2.04	0/0:6:3.55	0/0:12:5.35	0/0:4:2.95	0/0:4:2.94	0/0:2:2.34	0/0:1:2.04	0/0:11:5.05	0/0:2:2.34	./.	0/0:2:2.34	0/0:3:2.65	0/0:4:2.95	0/0:5:3.24	0/0:3:2.65	0/0:4:2.88	0/0:7:3.25	0/0:6:3.55	0/0:8:3.85	0/0:8:4.15	0/0:3:2.65	./.	0/0:1:2.04	0/0:4:2.94	0/0:3:2.65	0/0:3:2.65	0/0:4:2.95	0/0:3:2.65	0/0:2:2.34	0/0:3:2.65	0/0:1:2.04	0/0:2:2.34	0/0:4:2.95	0/0:3:2.65	0/0:2:2.34	0/0:7:3.55	0/0:2:2.34	0/0:5:3.25	0/0:6:3.55	0/0:4:2.95	0/0:3:2.41	0/0:4:2.95	0/0:1:2.04	0/0:6:3.55	0/0:1:2.04	0/0:3:2.65	0/0:3:2.65	0/0:4:2.94
+1	10000677	.	C	T	4.03	.	AF=0.01;NS=60;SB=-0.41	GT:RD:GQ	0/0:3:2.65	0/0:7:3.85	0/0:1:2.05	0/0:2:2.35	./.	0/0:5:3.23	0/0:5:3.19	0/0:1:2.05	0/0:5:3.25	0/0:3:2.65	0/0:3:2.65	0/0:1:2.04	0/0:1:2.05	0/0:7:3.83	0/0:11:5.05	0/0:4:2.95	0/0:6:3.05	0/0:1:2.05	0/0:2:2.33	0/0:10:4.68	0/0:2:2.05	./.	0/0:1:2.05	0/0:2:2.35	0/0:4:2.95	0/0:5:3.25	0/0:1:2.05	0/0:3:2.61	0/0:10:4.45	0/0:6:3.53	0/0:4:2.52	0/0:4:2.95	0/0:4:2.95	./.	0/0:2:2.35	0/0:5:3.09	0/0:1:2.04	0/0:3:2.65	0/1:4:0.67	0/0:3:2.65	0/0:3:2.64	0/0:2:2.35	0/0:1:2.05	0/0:2:2.30	0/0:3:2.61	0/0:4:2.95	0/0:3:2.65	0/0:7:3.85	0/0:3:2.65	0/0:7:3.85	0/0:6:3.55	0/0:4:2.95	0/0:3:2.57	0/0:2:2.35	./.	0/0:7:3.85	0/0:1:2.05	0/0:3:2.52	0/0:3:2.64	0/0:1:2.05
+1	10000700	.	T	C	2.21	.	AF=0.01;NS=60;SB=-0.23	GT:RD:GQ	0/0:1:2.06	0/0:8:4.16	./.	0/0:5:3.23	0/0:1:2.06	0/0:2:2.36	0/0:3:2.66	1/0:1:0.36	0/0:4:2.96	0/0:1:2.06	0/0:3:2.66	0/0:2:1.84	0/0:1:2.06	0/0:6:3.55	0/0:7:3.86	0/0:4:2.96	0/0:5:3.23	./.	0/0:2:2.36	0/0:4:2.96	0/0:1:2.05	0/0:2:2.34	./.	0/0:2:2.36	0/0:2:2.35	0/0:4:2.72	./.	0/0:2:2.36	0/0:6:3.45	0/0:3:2.66	0/0:6:3.54	0/0:4:2.96	0/0:1:2.06	./.	./.	0/0:1:1.54	0/0:1:2.06	0/0:3:2.66	0/0:4:2.96	0/0:3:2.65	0/0:4:2.96	./.	0/0:1:2.06	0/0:2:2.36	0/0:1:2.06	0/0:5:3.26	0/0:2:2.27	0/0:2:2.30	0/0:2:2.36	0/0:3:2.66	0/0:6:3.56	0/0:1:2.06	0/0:1:1.83	0/0:2:2.36	0/0:2:2.06	0/0:7:3.86	0/0:3:2.66	0/0:3:2.66	0/0:4:2.95	0/0:1:2.06
+1	10000708	.	C	T	0.00	.	AF=0.03;NS=60;SB=-0.83	GT:RD:GQ	0/0:1:1.59	0/0:9:3.97	./.	0/0:4:2.49	0/0:1:1.59	0/0:2:1.89	0/0:1:1.59	0/0:1:1.59	0/0:2:1.89	0/0:1:1.59	0/0:2:1.89	0/0:1:1.59	0/0:1:1.59	0/1:5:1.22	0/0:7:3.38	0/0:4:2.48	0/0:4:2.48	./.	0/0:2:1.89	0/0:2:1.89	0/0:1:1.58	0/0:2:1.85	0/0:1:1.59	0/0:2:1.89	0/0:2:1.89	0/0:2:1.89	./.	0/0:1:1.59	0/0:7:3.35	0/0:2:1.89	0/0:7:3.39	0/0:3:2.19	./.	./.	./.	./.	0/0:1:1.57	0/0:3:2.17	0/0:3:2.19	0/0:1:1.59	0/0:4:2.49	./.	0/0:1:1.59	0/0:2:1.89	0/0:2:1.89	0/0:3:2.19	0/0:1:1.59	0/0:1:1.59	0/0:3:2.19	0/0:4:2.49	0/0:6:3.08	0/0:2:1.89	0/1:2:1.52	0/0:2:1.88	0/0:3:2.19	0/0:6:3.08	0/0:2:1.89	0/0:3:2.19	0/0:6:3.08	0/0:1:1.59
+1	10000728	.	A	C	0.00	.	AF=0.02;NS=60;SB=2.53	GT:RD:GQ	0/0:1:1.77	0/0:6:2.08	0/0:1:1.77	0/0:2:2.08	0/0:1:1.77	0/0:1:1.77	./.	0/0:2:2.08	0/0:3:2.38	0/0:1:1.77	0/0:1:1.77	0/0:1:1.77	0/0:1:1.77	0/1:5:1.03	0/0:7:3.58	0/0:4:2.68	0/0:4:2.44	./.	0/0:1:1.77	0/0:2:2.08	0/0:1:1.77	0/0:1:1.77	0/0:1:1.77	0/0:4:2.68	0/0:2:2.08	0/0:3:2.38	0/0:4:2.68	0/0:1:1.77	0/0:4:2.68	0/0:2:2.08	0/0:2:2.07	0/0:7:3.57	./.	0/0:1:1.77	0/0:1:1.77	0/0:1:1.76	0/0:2:1.98	0/0:5:2.98	0/0:3:2.38	0/0:1:1.77	0/0:2:2.08	./.	./.	0/0:1:1.77	0/0:2:2.07	0/0:3:2.38	./.	./.	0/0:2:2.08	0/0:2:1.77	0/0:6:0.32	0/0:1:1.77	0/0:1:1.77	0/0:3:2.38	0/0:1:1.77	0/0:7:3.58	0/0:1:1.77	0/0:4:2.64	0/0:5:2.98	0/0:1:1.77
+1	10000730	.	A	G	2.11	.	AF=0.01;NS=60;SB=-0.22	GT:RD:GQ	0/0:1:2.01	0/0:6:2.99	0/0:2:2.32	0/0:2:2.31	0/0:1:2.01	0/0:2:2.30	./.	0/0:2:2.32	0/0:3:2.62	0/0:1:2.01	./.	0/0:2:2.30	0/0:1:2.01	0/1:5:0.34	0/0:7:3.82	0/0:4:2.91	0/0:4:2.49	./.	0/0:1:2.01	0/0:2:2.32	0/0:1:2.01	0/0:1:2.01	0/0:1:1.71	0/0:5:2.81	0/0:2:2.01	0/0:4:2.92	0/0:4:2.72	0/0:1:2.00	0/0:5:2.91	0/0:2:2.31	0/0:3:2.31	0/0:8:4.12	./.	0/0:1:2.01	0/0:1:2.01	0/0:1:1.50	0/0:2:2.08	0/0:5:3.22	0/0:3:2.62	0/0:1:2.01	0/0:2:2.32	./.	./.	0/0:2:2.32	0/0:2:2.19	0/0:3:2.62	./.	./.	0/0:3:2.62	0/0:2:2.31	0/0:6:3.52	0/0:1:2.01	./.	0/0:3:2.62	./.	0/0:7:3.82	0/0:1:2.01	0/0:4:2.86	0/0:5:3.22	0/0:1:2.01
+1	10000734	.	G	A	0.00	.	AF=0.01;NS=60;SB=2.19	GT:RD:GQ	0/0:2:2.17	0/0:6:3.32	0/0:2:2.17	./.	0/0:1:1.87	0/0:2:2.17	./.	0/0:2:1.57	0/0:3:2.47	0/0:1:1.87	./.	0/0:2:2.11	0/0:1:1.87	0/0:6:3.37	0/0:7:3.67	0/0:4:2.77	0/0:5:2.75	./.	0/0:1:1.87	0/0:2:2.17	0/0:3:2.47	./.	./.	0/0:5:3.08	0/0:2:2.17	0/0:5:3.06	0/0:5:3.07	0/0:1:1.86	0/0:5:3.08	0/0:2:2.17	0/0:2:2.17	0/0:9:4.18	./.	0/0:1:1.87	0/0:2:2.17	0/0:1:1.85	0/0:2:2.03	0/0:5:3.08	0/0:3:2.47	0/0:1:1.87	0/0:1:1.87	./.	./.	0/0:1:1.87	0/0:3:2.47	1/0:3:1.30	0/0:1:1.87	0/0:1:1.85	0/0:3:2.47	0/0:2:1.65	0/0:6:3.37	0/0:1:1.87	./.	0/0:3:2.47	./.	0/0:6:3.37	0/0:1:1.87	0/0:4:2.76	0/0:5:3.07	0/0:1:1.87
+1	10000736	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.39	GT:RD:GQ	0/0:2:2.20	0/0:6:3.38	0/0:3:2.19	./.	0/0:2:1.89	0/0:2:2.19	./.	./.	0/0:3:2.50	0/0:1:1.89	./.	0/0:2:2.07	0/0:2:2.19	0/0:6:3.27	0/0:7:3.70	0/0:4:2.80	0/0:4:2.79	0/0:1:1.59	0/0:1:1.89	0/0:2:2.18	0/0:3:2.50	./.	./.	0/0:5:3.10	0/0:2:2.20	0/0:5:3.10	0/0:5:3.09	0/0:1:1.89	0/0:4:2.79	0/0:2:2.19	0/0:2:2.20	0/0:9:4.29	./.	0/0:1:1.89	0/0:2:2.19	0/0:1:1.88	0/0:1:1.89	0/0:5:3.10	0/0:3:2.50	0/0:1:1.89	0/0:1:1.89	./.	./.	0/0:1:1.89	0/0:3:2.37	1/0:3:1.05	0/0:1:1.89	0/0:1:1.89	0/0:3:2.50	0/0:2:1.83	0/0:6:3.40	0/0:1:1.89	./.	0/0:3:2.50	./.	0/0:6:3.40	0/0:1:1.89	0/0:5:2.79	0/0:5:3.09	0/0:1:1.89
+1	10000737	.	G	A	0.00	.	AF=0.01;NS=60;SB=2.20	GT:RD:GQ	0/0:2:2.19	0/0:6:3.21	0/0:2:2.19	./.	0/0:2:2.19	0/0:2:2.19	./.	./.	0/0:3:2.49	0/0:2:2.19	./.	0/0:2:2.19	0/0:2:2.19	0/0:5:3.09	0/0:7:3.69	0/0:4:2.79	0/0:4:2.79	0/0:1:1.89	0/0:1:1.89	0/0:2:2.19	0/0:3:2.49	./.	./.	0/0:5:3.09	0/0:2:2.19	0/0:4:2.78	0/0:6:3.39	0/0:1:1.88	0/0:4:2.49	0/0:2:2.19	0/0:2:2.19	0/0:8:3.96	./.	0/0:1:1.89	0/0:2:2.17	0/0:1:1.73	0/0:1:1.89	0/0:5:3.09	0/0:3:2.49	0/0:1:1.89	0/0:1:1.89	./.	./.	0/0:1:1.89	0/0:3:2.49	1/0:3:1.28	0/0:1:1.89	0/0:1:1.88	0/0:3:2.49	0/0:2:1.89	0/0:6:3.39	0/0:2:2.19	./.	0/0:3:2.49	./.	0/0:6:3.39	0/0:1:1.89	0/0:5:3.07	0/0:5:3.09	0/0:1:1.89
+1	10000739	.	A	G	0.00	.	AF=0.05;NS=60;SB=0.22	GT:RD:GQ	0/0:2:1.60	0/0:6:2.78	0/0:3:1.60	./.	0/0:2:1.60	0/0:2:1.59	./.	./.	0/0:3:1.90	0/0:2:1.59	./.	0/0:2:1.56	0/0:2:1.60	0/1:5:1.05	0/0:7:3.10	0/0:4:2.20	0/0:4:2.18	0/0:1:1.30	0/0:1:1.30	0/0:2:1.60	0/0:3:1.90	./.	0/0:1:0.99	0/0:4:2.20	0/0:2:1.60	0/0:4:1.88	0/0:6:2.49	0/0:2:1.60	0/0:3:1.89	0/0:2:1.60	0/0:2:1.60	0/0:8:3.39	./.	0/0:1:1.30	0/0:2:1.30	0/0:1:0.78	0/0:2:0.82	0/0:5:2.50	0/0:3:1.90	./.	0/0:1:1.30	./.	./.	0/0:1:1.30	0/0:3:1.90	0/1:3:1.55	0/0:1:1.29	0/0:1:1.29	0/0:3:1.90	0/0:1:1.30	0/1:6:0.34	0/0:2:1.60	./.	0/0:3:1.90	./.	0/1:6:0.54	0/0:1:1.30	0/0:5:2.40	0/0:4:2.16	0/0:1:1.30
+1	10000740	.	C	T	0.00	.	AF=0.01;NS=60;SB=-0.21	GT:RD:GQ	0/0:2:2.18	0/1:6:1.51	0/0:3:2.48	./.	0/0:2:2.18	0/0:2:2.17	./.	./.	0/0:3:2.48	0/0:2:2.14	./.	0/0:2:2.17	0/0:2:2.18	0/0:5:3.09	0/0:7:3.68	0/0:4:2.79	0/0:4:2.79	0/0:1:1.88	0/0:1:1.88	0/0:2:2.18	0/0:3:2.48	./.	0/0:1:1.88	0/0:4:2.79	0/0:2:2.18	0/0:5:3.07	0/0:5:3.08	0/0:2:2.18	0/0:3:2.48	0/0:2:2.18	0/0:1:1.88	0/0:8:3.98	./.	0/0:1:1.88	0/0:1:1.88	0/0:1:1.88	0/0:2:2.16	0/0:5:3.08	0/0:3:2.48	./.	0/0:1:1.88	./.	./.	0/0:1:1.88	0/0:3:2.48	0/0:3:2.48	0/0:1:1.88	0/0:1:1.85	0/0:3:2.48	0/0:1:1.88	0/0:6:3.38	0/0:2:2.18	./.	0/0:3:2.48	./.	0/0:6:3.38	0/0:1:1.88	0/0:5:2.98	0/0:4:2.79	0/0:1:1.88
+1	10000745	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.48	GT:RD:GQ	0/0:2:2.22	0/0:5:3.11	0/0:3:2.52	./.	0/0:1:1.92	0/0:2:2.21	./.	./.	0/0:4:2.80	0/0:2:2.22	./.	0/0:2:2.18	0/0:2:2.20	0/0:6:3.42	0/0:7:3.72	0/0:5:3.12	0/0:6:3.42	0/0:1:1.92	0/0:1:1.92	0/0:2:2.22	0/0:3:2.52	./.	0/0:1:1.92	0/0:5:3.12	0/0:2:2.22	0/0:7:3.72	0/0:6:2.11	0/0:2:2.21	0/0:4:2.71	0/0:2:2.22	0/0:1:1.92	0/0:8:4.01	./.	0/0:1:1.92	0/0:2:2.22	0/0:1:1.92	0/0:2:2.19	0/0:5:3.12	0/0:3:2.52	./.	0/0:1:1.92	./.	./.	0/0:1:1.40	0/0:4:2.82	1/0:3:0.92	0/0:2:2.21	0/0:2:2.21	0/0:4:2.82	0/0:2:1.92	0/0:6:3.42	0/0:2:2.20	0/0:1:1.62	0/0:3:2.52	./.	0/0:6:3.42	0/0:1:1.92	0/0:5:3.09	0/0:3:2.39	0/0:1:1.92
+1	10000748	.	T	C	0.00	.	AF=0.02;NS=60;SB=2.32	GT:RD:GQ	0/0:2:1.18	0/0:6:3.13	0/0:3:2.24	./.	0/0:1:1.63	0/0:2:1.89	./.	./.	0/0:4:2.50	0/0:1:1.63	./.	0/0:2:1.93	0/0:2:1.93	1/0:6:0.30	0/0:7:3.44	0/0:5:2.84	0/0:7:2.84	0/0:1:1.63	0/0:1:1.63	0/0:3:2.20	0/0:3:2.24	./.	0/0:1:1.63	0/0:5:2.84	0/0:2:1.94	0/0:7:2.97	0/0:6:2.57	0/0:2:1.93	0/0:4:2.54	0/0:2:1.94	0/0:1:1.63	0/0:9:4.00	./.	0/0:1:1.63	0/0:2:1.94	0/0:1:1.63	0/0:2:1.80	0/0:5:2.84	0/0:2:1.94	./.	0/0:1:1.63	./.	./.	0/0:2:1.93	0/0:5:2.84	1/0:3:1.21	0/0:2:1.80	0/0:2:1.93	0/0:3:2.24	0/0:2:1.94	0/0:6:3.14	0/0:2:1.93	0/0:1:1.63	0/0:3:2.24	./.	0/0:6:3.14	0/0:2:1.94	0/0:5:2.82	0/0:3:0.68	0/0:1:1.63
+1	10000750	.	G	A,C,T	0.00	.	AF=0.03;NS=60;SB=0.90	GT:RD:GQ	0/0:2:1.78	0/0:5:1.18	0/0:3:2.08	./.	0/0:1:1.47	0/0:2:1.78	./.	./.	0/0:3:2.07	0/0:1:1.47	./.	0/0:2:1.77	0/0:2:1.78	1/0:6:0.16	0/0:7:3.28	0/0:5:2.68	0/0:5:2.68	0/0:1:1.47	0/0:1:1.47	0/0:3:1.72	0/0:3:2.07	./.	0/0:1:1.47	2/0:6:0.24	0/0:2:1.78	0/0:7:3.28	0/0:7:1.59	0/0:1:1.47	0/0:4:2.15	0/0:2:1.78	0/0:1:1.47	0/0:9:3.85	./.	0/0:1:1.47	0/0:2:1.67	0/0:1:1.47	0/0:2:0.82	0/0:6:2.98	0/0:2:1.78	./.	0/0:1:1.47	./.	./.	0/0:2:1.77	0/0:5:2.68	2/0:3:2.30	0/0:2:1.78	0/0:2:1.77	0/0:3:2.08	0/0:2:1.78	0/3:6:0.19	0/0:2:1.77	0/0:2:1.77	0/0:3:2.08	./.	2/0:6:0.50	0/0:2:1.78	0/0:5:2.67	0/0:4:2.37	0/0:1:1.47
+1	10000752	.	C	T	0.00	.	AF=0.02;NS=60;SB=-0.15	GT:RD:GQ	0/0:2:1.94	0/0:5:2.80	0/0:3:2.24	./.	0/0:1:1.64	0/0:2:1.84	./.	0/0:1:1.34	0/0:3:0.98	0/0:1:1.64	0/0:2:1.34	0/0:2:1.86	0/0:2:1.91	0/0:6:3.13	0/0:7:3.43	0/0:5:2.84	0/0:5:2.84	0/0:1:1.64	0/0:1:1.64	0/0:3:2.10	0/0:3:2.24	./.	0/0:1:1.64	0/0:5:2.84	0/0:2:1.94	0/0:7:3.40	0/0:7:3.35	0/0:1:1.64	0/0:4:2.53	0/0:2:1.94	0/0:1:1.64	0/0:10:4.29	./.	0/0:1:1.64	0/0:2:1.94	0/0:1:1.64	0/0:1:1.63	0/0:6:3.14	0/0:2:1.94	./.	0/0:1:1.64	./.	./.	0/0:2:1.94	0/0:5:2.69	0/1:3:1.48	0/0:2:1.93	0/0:2:1.91	0/0:3:2.23	0/0:2:1.94	0/0:6:3.14	0/0:2:1.83	0/0:2:1.91	0/0:3:2.24	./.	0/1:6:0.33	0/0:1:1.64	0/0:5:2.81	0/0:3:2.24	0/0:1:1.64
+1	10000753	.	G	A	1.23	.	AF=0.01;NS=60;SB=-0.11	GT:RD:GQ	0/0:2:2.46	0/0:5:3.19	0/0:3:2.47	./.	0/0:1:2.16	0/0:2:2.38	./.	0/0:1:2.16	0/0:3:2.58	0/0:1:2.16	0/0:2:2.47	0/0:2:2.12	0/0:2:2.46	1/0:6:0.10	0/0:7:3.95	0/0:5:3.37	0/0:5:3.37	0/0:1:2.16	0/0:1:2.16	0/0:3:2.72	0/0:3:2.77	./.	0/0:1:2.16	0/0:5:3.06	0/0:2:2.45	0/0:7:3.97	0/0:8:4.02	0/0:1:2.16	0/0:4:3.07	0/0:2:2.46	0/0:1:2.16	0/0:10:4.84	./.	0/0:1:2.16	0/0:2:2.47	0/0:1:2.16	0/0:1:2.16	0/0:6:3.67	0/0:2:2.46	./.	0/0:1:2.16	./.	./.	0/0:2:2.46	0/0:5:3.22	0/0:3:2.76	0/0:2:2.46	0/0:2:2.45	0/0:3:2.76	0/0:2:2.46	0/0:6:3.67	0/0:2:2.45	0/0:2:2.47	0/0:4:3.06	./.	0/0:6:3.66	0/0:1:2.16	0/0:5:3.33	0/0:4:2.89	0/0:1:2.16
+1	10000755	.	C	A	0.00	.	AF=0.01;NS=60;SB=1.97	GT:RD:GQ	0/0:2:2.20	0/0:4:2.31	0/0:2:2.20	./.	0/0:1:1.90	0/0:2:2.20	./.	0/0:1:1.90	0/0:4:2.80	0/0:2:2.20	0/0:2:2.20	0/0:2:2.19	0/0:2:2.20	0/0:6:3.40	0/0:7:3.71	0/0:5:3.10	0/0:6:3.06	0/0:1:1.90	0/0:1:1.90	0/0:3:2.50	0/0:3:2.50	./.	0/0:1:1.90	0/0:4:2.80	0/0:2:2.20	0/0:6:3.40	0/0:8:3.47	0/0:1:1.88	0/0:4:2.66	0/0:2:2.20	0/0:1:1.90	0/0:9:4.30	./.	0/0:1:1.90	0/0:2:1.83	0/0:1:1.90	0/0:1:1.90	0/0:6:3.41	0/0:1:1.90	./.	0/0:1:1.90	./.	./.	0/0:2:2.20	0/0:5:3.02	1/0:3:1.53	0/0:2:2.20	0/0:2:2.17	0/0:4:2.80	0/0:2:2.20	0/0:6:3.40	0/0:2:2.07	0/0:2:2.05	0/0:4:2.80	./.	0/0:6:3.41	0/0:1:1.90	0/0:5:3.10	0/0:3:2.46	./.
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+1	10000760	.	G	A	0.00	.	AF=0.02;NS=60;SB=0.33	GT:RD:GQ	0/0:2:1.94	0/0:4:2.51	0/0:1:1.64	0/0:1:1.64	0/0:1:1.34	0/0:2:1.94	./.	0/0:1:1.64	0/0:4:2.30	0/0:2:1.94	0/0:2:1.80	0/0:2:1.91	0/0:2:1.93	1/0:5:1.02	0/0:6:3.14	0/0:5:2.84	0/0:6:3.15	0/0:1:1.34	0/0:1:1.64	0/0:2:1.93	0/0:2:1.94	./.	0/0:1:1.64	0/0:5:2.84	0/0:2:1.94	0/0:7:3.44	0/0:7:3.43	0/0:1:1.64	0/0:2:1.93	0/0:2:1.94	0/0:1:1.64	0/0:9:4.00	./.	0/0:1:1.64	0/0:2:1.94	0/0:1:1.64	0/0:1:1.64	0/0:6:3.15	0/0:1:1.64	./.	0/0:1:1.64	./.	./.	0/0:2:1.94	0/0:5:2.84	0/0:3:2.24	0/0:2:1.94	0/0:1:1.64	0/0:4:2.45	0/0:2:1.94	0/0:6:3.14	0/0:1:1.64	0/0:2:1.47	0/0:4:2.54	0/0:1:1.34	1/0:6:0.48	0/0:1:1.64	0/0:5:2.54	0/0:3:2.24	./.
+1	10000762	.	C	T	0.00	.	AF=0.02;NS=60;SB=1.47	GT:RD:GQ	0/0:2:1.88	0/0:4:2.48	0/0:1:1.59	0/0:1:1.59	./.	0/0:2:1.89	./.	0/0:1:1.59	0/0:4:2.44	0/0:2:1.89	0/0:2:1.89	0/0:2:1.73	0/0:2:1.88	0/0:5:2.79	0/0:6:3.09	0/0:5:2.79	0/0:6:3.09	./.	0/0:1:1.59	0/0:2:1.89	0/0:2:1.88	./.	0/0:1:1.59	0/0:5:2.79	0/0:2:1.89	0/1:6:1.26	0/0:7:3.38	0/0:1:1.59	0/0:2:1.89	0/0:2:1.89	0/0:2:1.59	0/0:8:3.67	./.	0/1:1:1.46	0/0:2:1.89	0/0:1:1.59	0/0:1:1.59	0/0:6:3.10	0/0:1:1.59	./.	0/0:1:1.59	./.	./.	0/0:2:1.89	0/0:5:2.79	0/0:3:2.19	0/0:2:1.85	0/0:1:1.59	0/0:4:2.49	0/0:2:1.89	0/0:6:3.09	0/0:1:1.59	0/0:3:2.19	0/0:4:2.49	0/0:1:1.59	0/0:6:3.09	0/0:1:1.59	0/0:4:2.49	0/0:3:2.19	./.
+1	10000763	.	C	T	1.98	.	AF=0.01;NS=60;SB=-0.21	GT:RD:GQ	0/0:2:2.35	0/0:4:1.83	0/0:1:1.76	0/0:2:2.36	./.	0/0:2:2.36	./.	0/0:1:2.06	0/0:5:3.25	0/0:2:2.36	0/0:2:2.36	0/0:2:2.35	0/0:2:2.36	0/0:5:3.26	0/0:6:3.56	0/0:5:3.26	0/0:6:3.56	./.	0/0:1:2.06	0/0:2:2.35	0/0:2:2.36	./.	0/0:1:1.76	0/1:5:0.30	0/0:2:2.36	0/0:6:3.23	0/0:7:3.85	0/0:1:2.06	0/0:2:2.36	0/0:2:2.36	0/0:2:2.35	0/0:8:4.16	./.	0/0:1:2.06	0/0:2:2.36	0/0:1:2.06	0/0:1:2.06	0/0:6:3.56	0/0:1:2.06	./.	0/0:1:2.06	./.	./.	0/0:2:2.36	0/0:5:3.07	0/0:3:2.66	0/0:2:2.36	0/0:1:2.06	0/0:4:2.96	0/0:2:2.36	0/0:6:3.56	0/0:1:2.06	0/0:3:2.66	0/0:4:2.96	0/0:1:2.06	0/0:6:3.56	0/0:1:2.06	0/0:4:2.96	0/0:3:2.66	./.
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+1	10000785	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.01	GT:RD:GQ	0/0:1:1.85	0/0:2:2.15	./.	0/0:3:2.44	./.	0/0:1:1.85	./.	0/0:1:1.85	0/0:4:2.75	0/0:2:2.14	./.	./.	0/0:1:1.85	0/0:5:3.05	0/0:5:3.05	0/0:6:3.35	0/0:2:2.15	0/0:2:2.15	0/0:4:2.35	0/0:6:3.35	0/0:1:1.85	./.	0/0:1:1.85	0/0:2:2.15	0/0:1:1.85	0/0:3:2.45	0/0:6:3.35	0/0:1:1.85	0/0:1:1.85	0/0:2:2.15	0/0:3:2.42	0/0:2:2.14	./.	./.	0/0:1:1.85	./.	0/0:1:1.85	0/0:6:3.35	0/0:1:1.85	./.	0/0:2:2.15	0/0:2:2.15	0/1:1:1.52	0/0:1:1.85	0/0:5:2.92	0/0:3:2.45	0/0:1:1.85	0/0:2:2.15	0/0:5:2.97	0/0:2:2.11	0/0:6:3.35	0/0:1:1.55	0/0:1:1.85	0/0:5:3.05	./.	0/0:7:3.65	./.	0/0:1:1.85	0/0:3:2.45	0/0:3:2.45
+1	10000798	.	T	C	1.34	.	AF=0.01;NS=60;SB=-0.14	GT:RD:GQ	0/0:1:2.10	0/0:3:2.70	0/0:1:2.10	0/0:4:3.00	./.	0/0:2:2.40	./.	./.	0/0:4:3.00	0/0:2:2.40	0/0:1:2.10	./.	./.	1/0:5:0.14	0/0:4:3.00	0/0:6:3.61	0/0:3:2.70	0/0:1:2.10	0/0:5:3.31	0/0:7:3.91	./.	0/0:1:2.10	0/0:1:2.10	0/0:3:2.70	0/0:1:2.10	0/0:3:2.70	0/0:4:3.00	0/0:2:2.40	0/0:2:2.40	0/0:2:2.10	0/0:2:2.15	0/0:3:2.70	./.	./.	0/0:1:2.10	0/0:1:2.10	0/0:2:2.40	0/0:6:3.61	0/0:3:2.70	./.	0/0:2:2.40	0/0:3:2.70	0/0:2:2.40	./.	0/0:2:2.40	0/0:3:2.70	./.	0/0:2:2.40	0/0:6:3.60	0/0:2:2.39	0/0:6:3.61	./.	./.	0/0:4:3.00	./.	0/0:5:3.30	0/0:1:2.10	0/0:2:2.40	0/0:3:2.70	0/0:4:3.00
+1	10000802	.	C	A,G	0.00	.	AF=0.01;NS=60;SB=2.46	GT:RD:GQ	0/0:1:1.88	0/0:4:0.73	0/0:1:1.88	0/0:4:2.78	./.	0/0:2:2.18	./.	0/0:1:1.76	0/0:4:2.77	0/0:2:2.18	0/0:1:1.88	./.	./.	0/0:5:3.08	0/0:4:2.78	0/0:6:3.39	0/0:3:2.48	0/0:1:1.88	0/0:5:3.08	0/0:6:3.38	./.	0/0:1:1.88	0/0:1:1.88	0/0:3:2.48	0/0:1:1.88	0/0:3:2.48	0/0:4:2.42	0/0:2:2.18	0/0:2:2.18	0/0:2:2.18	0/0:1:1.88	0/0:2:2.18	./.	./.	0/0:1:1.88	0/0:1:1.88	0/0:2:2.18	0/0:7:3.69	0/0:3:2.48	./.	0/0:2:2.18	0/0:3:2.48	0/0:1:1.88	./.	0/0:1:1.88	0/0:3:2.48	./.	0/0:2:2.18	0/0:6:3.39	1/0:2:0.12	0/0:6:3.39	./.	./.	0/0:4:2.78	./.	0/2:5:0.99	0/0:1:1.88	0/0:2:2.18	0/0:3:2.48	0/0:3:2.48
+1	10000805	.	A	G,T	0.00	.	AF=0.01;NS=60;SB=0.57	GT:RD:GQ	0/0:1:1.90	0/0:4:2.46	0/0:1:1.90	0/0:4:2.80	./.	0/0:2:2.20	./.	0/0:1:1.79	0/0:3:2.50	0/0:2:2.20	0/0:1:1.90	./.	./.	0/0:5:3.10	0/0:4:2.80	0/0:6:3.40	0/0:3:2.50	0/0:1:1.90	0/0:5:3.10	0/0:6:3.40	./.	0/0:1:1.90	0/0:1:1.90	0/0:2:2.20	0/0:1:1.90	0/0:3:2.50	0/0:3:2.50	0/0:2:2.09	0/0:1:1.90	0/0:2:2.20	0/0:2:2.19	0/0:1:1.90	./.	./.	./.	0/0:2:2.19	0/0:2:2.20	0/0:7:3.70	0/0:3:2.50	./.	0/0:2:2.20	0/0:2:2.20	0/0:1:1.90	./.	0/0:2:2.20	0/1:3:0.25	./.	0/0:2:2.20	0/0:6:3.38	0/0:1:1.89	0/0:6:0.36	./.	./.	0/0:4:2.80	0/0:1:1.90	0/2:5:0.50	0/0:1:1.90	0/0:4:2.80	0/0:2:2.20	0/0:4:2.80
+1	10000809	.	G	A	1.15	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:1:2.15	0/0:4:2.99	0/0:1:2.15	0/0:3:2.75	./.	0/0:3:2.75	./.	0/0:1:2.14	0/0:3:2.74	0/0:1:2.15	0/0:2:2.45	0/0:1:2.15	./.	0/0:5:3.19	0/0:4:3.05	0/0:6:3.65	0/0:3:2.75	0/0:1:2.15	0/0:5:3.35	0/0:6:3.65	./.	0/0:1:2.15	0/0:1:2.15	0/0:2:2.45	0/0:1:2.15	0/0:3:2.75	0/0:3:2.75	0/0:4:2.75	0/0:2:2.45	0/0:2:2.45	0/0:5:2.74	0/0:1:2.15	./.	./.	./.	0/0:2:2.45	0/0:2:2.45	0/0:7:3.95	0/0:3:2.75	./.	0/0:2:2.45	0/0:2:2.45	0/0:1:2.15	./.	0/0:2:2.45	0/0:3:2.75	./.	0/0:2:2.45	0/0:4:3.04	0/0:1:2.13	0/0:6:3.65	./.	./.	0/0:4:3.05	0/0:1:2.15	1/0:5:0.07	0/0:1:2.15	0/0:4:3.05	0/0:3:2.75	0/0:2:2.45
+1	10000811	.	T	C	0.00	.	AF=0.02;NS=60;SB=0.36	GT:RD:GQ	0/0:1:1.61	0/0:4:2.48	0/0:1:1.61	0/0:3:2.21	./.	0/0:3:2.20	./.	0/0:2:1.91	0/0:3:2.21	0/0:1:1.61	0/0:2:1.85	0/0:1:1.61	./.	1/0:5:0.63	0/0:3:2.21	0/0:6:3.11	0/0:3:2.21	0/0:1:1.61	0/0:5:2.73	0/0:6:2.29	./.	0/0:1:1.61	0/0:2:1.33	0/0:3:1.91	0/0:1:1.61	0/0:3:2.21	0/0:3:2.12	0/0:4:2.31	0/0:2:1.91	0/0:2:1.91	0/0:5:2.61	0/0:1:1.61	./.	./.	./.	0/0:2:1.91	0/0:2:1.91	0/0:7:3.41	0/0:3:2.21	0/0:1:1.31	0/0:2:1.91	0/0:2:1.91	0/0:1:1.61	./.	0/0:2:1.91	0/0:3:2.21	./.	0/0:2:1.88	0/0:4:2.48	0/0:1:1.59	0/0:6:0.47	./.	./.	0/0:4:2.51	0/0:1:1.61	1/0:5:0.33	./.	0/0:4:2.51	0/0:3:2.21	0/0:2:1.87
+1	10000812	.	G	A	0.00	.	AF=0.02;NS=60;SB=0.18	GT:RD:GQ	0/0:1:1.63	0/0:4:2.53	0/0:1:1.63	0/0:3:2.23	./.	0/0:3:2.21	./.	0/0:2:1.92	0/0:3:2.23	0/0:2:1.93	0/0:2:1.82	0/0:2:1.91	./.	1/0:5:0.94	0/0:3:2.23	0/0:6:3.13	0/0:3:2.23	0/0:1:1.63	0/0:5:2.83	0/0:6:3.12	./.	0/0:2:1.93	0/0:2:1.93	0/0:3:2.23	0/0:1:1.63	0/0:3:2.23	0/0:3:2.23	0/0:4:2.23	0/0:2:1.93	0/0:2:1.93	0/0:5:2.50	0/0:1:1.63	./.	./.	./.	0/0:2:1.93	0/0:2:1.93	0/0:7:3.44	0/0:3:2.23	0/0:1:1.63	0/0:2:1.93	0/0:2:1.93	0/0:1:1.63	./.	0/0:2:1.93	0/0:3:2.23	./.	0/0:2:1.63	0/0:4:2.52	0/0:1:1.60	0/0:6:3.13	./.	./.	0/0:4:2.53	0/0:1:1.63	1/0:5:0.69	./.	0/0:4:2.53	0/0:3:2.23	0/0:2:1.93
+1	10000813	.	G	C	2.67	.	AF=0.01;NS=60;SB=-0.28	GT:RD:GQ	0/0:1:2.02	0/0:4:2.92	0/0:2:2.02	0/0:3:2.62	./.	0/0:3:2.62	./.	0/0:2:2.32	0/0:3:2.62	0/0:2:2.32	0/0:3:2.32	1/0:2:0.46	./.	0/0:5:3.22	0/0:3:2.62	0/0:6:3.53	0/0:3:2.62	0/0:1:2.02	0/0:5:3.23	0/0:5:3.23	0/0:1:2.02	0/0:2:2.32	0/0:2:2.32	0/0:3:2.62	0/0:1:2.02	0/0:3:2.62	0/0:3:2.62	0/0:3:2.62	0/0:2:2.32	0/0:3:2.62	0/0:5:3.22	0/0:1:2.02	./.	./.	./.	0/0:2:2.21	0/0:2:2.32	0/0:7:3.83	0/0:3:2.62	0/0:1:2.02	0/0:2:2.32	0/0:2:2.32	0/0:2:2.02	./.	0/0:2:2.32	0/0:3:2.62	./.	0/0:1:2.02	0/0:4:2.92	0/0:1:2.02	0/0:6:3.53	./.	0/0:1:2.02	0/0:4:2.92	0/0:1:2.02	0/0:5:3.23	./.	0/0:4:2.92	0/0:3:2.62	0/0:2:2.32
+1	10000817	.	T	C,G	0.00	.	AF=0.02;NS=60;SB=-0.17	GT:RD:GQ	0/0:2:2.06	0/0:4:2.15	0/0:1:1.76	0/0:2:2.06	./.	0/0:3:1.55	./.	0/0:2:2.06	0/0:2:2.06	0/0:2:2.05	0/0:4:2.60	0/0:2:2.06	./.	0/0:5:2.97	0/0:3:2.37	0/0:6:3.27	0/0:3:2.36	0/0:1:1.76	0/0:4:2.48	0/0:5:2.45	0/0:1:1.76	0/0:2:2.06	0/0:2:0.66	0/0:3:2.37	0/0:1:1.76	0/0:3:2.36	0/0:4:2.61	0/0:3:2.36	0/0:2:2.06	1/0:3:0.10	0/0:5:2.95	0/0:1:1.76	./.	./.	./.	0/0:2:2.06	0/0:2:2.06	0/0:7:3.57	0/0:3:2.37	0/0:2:2.06	0/0:2:2.06	2/0:2:0.76	0/0:3:2.36	./.	0/0:2:2.06	0/0:3:2.37	0/0:1:1.76	0/0:1:1.46	0/0:3:1.93	./.	0/0:6:3.27	./.	0/0:1:1.76	1/0:4:0.48	0/0:1:1.76	0/0:5:2.66	./.	0/0:3:2.37	0/0:3:2.36	0/0:2:1.63
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+1	10000851	.	G	A,T	2.98	.	AF=0.01;NS=60;SB=-3.00	GT:RD:GQ	0/0:4:2.97	0/0:7:3.29	0/0:1:2.07	0/0:2:2.37	0/0:1:2.07	0/0:1:2.07	./.	0/0:1:2.07	0/0:4:2.96	1/0:3:0.09	0/0:7:3.85	0/0:5:3.24	./.	0/0:4:2.97	0/0:3:2.67	0/0:6:3.57	0/0:5:3.27	0/0:1:2.07	0/0:1:2.07	0/0:1:2.06	0/0:2:1.36	./.	0/0:2:2.36	0/0:2:2.37	0/0:2:2.37	0/0:3:2.67	0/0:3:2.63	0/0:2:2.37	0/0:5:3.21	0/0:3:2.67	0/0:4:2.97	0/0:3:2.64	0/0:1:2.07	./.	0/0:1:2.07	0/0:2:2.37	./.	0/0:7:3.86	0/0:2:2.37	0/0:5:3.26	0/0:3:2.67	0/0:2:2.37	0/0:1:2.02	0/0:1:2.07	0/0:3:2.66	0/0:3:2.67	0/0:3:2.18	0/0:4:2.97	0/0:5:3.27	0/0:1:1.77	0/2:6:0.26	0/0:3:2.18	0/0:1:2.07	0/0:5:3.27	0/0:1:2.07	0/0:5:3.27	./.	0/0:1:2.07	0/0:3:1.91	./.
+1	10000856	.	G	T	0.00	.	AF=0.01;NS=60;SB=2.74	GT:RD:GQ	0/0:3:2.60	0/0:6:3.50	0/0:1:2.00	0/0:2:2.30	0/0:1:2.00	0/0:1:1.79	./.	./.	0/0:4:2.90	0/0:3:2.28	0/0:7:3.80	0/0:5:3.18	./.	0/0:4:2.90	0/0:3:2.60	0/0:6:3.50	0/0:5:3.20	./.	0/0:1:2.00	0/0:1:2.00	0/0:2:2.29	./.	0/0:2:1.34	0/0:2:2.30	0/0:2:2.30	0/0:3:2.60	0/0:3:2.50	0/0:2:2.30	0/0:7:3.80	0/0:3:2.60	0/0:5:2.90	0/0:3:2.59	0/0:1:1.99	./.	0/0:1:1.89	0/0:1:2.00	0/0:1:2.00	0/0:6:3.50	0/0:2:2.30	0/0:3:2.54	0/0:3:2.60	0/0:2:2.30	0/0:1:2.00	0/0:1:2.00	0/0:3:2.54	0/0:3:2.60	0/0:3:1.38	0/0:4:2.90	0/0:5:3.20	0/0:1:2.00	0/1:6:0.43	0/0:3:2.31	0/0:1:2.00	0/0:5:3.20	0/0:1:2.00	0/0:5:3.20	./.	0/0:1:2.00	0/0:3:2.60	./.
+1	10000857	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.57	GT:RD:GQ	0/0:3:2.56	0/0:7:3.64	0/0:1:1.96	0/0:2:2.26	0/0:1:1.96	./.	./.	./.	0/0:4:2.86	0/0:3:2.44	0/0:7:3.46	0/0:5:2.99	./.	0/1:4:0.77	0/0:3:2.56	0/0:6:3.46	0/0:5:3.15	./.	0/0:1:1.96	0/0:1:1.93	0/0:2:2.14	./.	0/0:2:1.82	0/0:2:2.26	0/0:2:2.26	0/0:4:2.56	0/0:3:2.56	0/0:3:2.56	0/0:7:3.42	0/0:4:2.85	0/0:4:2.86	0/0:3:2.50	0/0:1:1.96	./.	0/0:2:1.96	0/0:1:1.96	0/0:1:1.96	0/0:6:3.46	0/0:2:2.26	0/0:3:2.23	0/0:3:2.56	0/0:2:2.26	0/0:1:1.96	0/0:1:1.96	0/0:3:2.51	0/0:3:2.56	0/0:3:2.54	0/0:4:2.86	0/0:5:3.16	0/0:1:1.96	0/0:6:3.45	0/0:3:2.17	0/0:1:1.96	0/0:5:3.16	0/0:1:1.96	0/0:5:3.16	./.	0/0:1:1.96	0/0:3:2.37	./.
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+1	10000872	.	C	T,G	0.00	.	AF=0.01;NS=60;SB=0.30	GT:RD:GQ	0/0:3:2.53	0/0:7:3.75	0/0:1:1.96	0/0:2:2.26	./.	./.	0/0:2:2.26	0/0:2:2.26	0/0:5:0.49	0/0:5:2.30	0/0:3:2.56	0/0:2:2.26	./.	0/1:4:0.96	0/0:4:2.86	0/0:6:3.46	0/0:5:3.14	0/0:2:2.22	0/0:2:2.26	0/0:1:1.96	0/0:2:1.72	0/0:2:2.26	0/0:4:2.54	0/0:1:1.96	0/0:2:2.26	0/0:2:2.20	0/0:3:2.25	0/0:3:2.56	0/0:5:3.16	0/0:4:2.86	0/0:5:3.15	0/0:6:3.41	0/0:1:1.96	0/0:1:1.77	0/0:3:2.56	0/0:1:1.96	0/0:1:1.96	0/0:7:3.76	0/0:2:2.26	0/2:2:0.31	0/0:2:2.26	0/0:1:1.96	0/0:2:2.26	0/0:1:1.96	0/0:5:3.15	0/0:3:2.56	0/0:3:2.17	0/0:4:2.80	0/0:7:3.70	0/0:2:2.26	0/0:6:3.46	0/0:2:2.25	0/0:1:1.96	0/0:4:2.86	0/0:1:1.75	0/0:5:3.16	./.	0/0:3:2.07	0/0:1:1.96	./.
+1	10000874	.	G	A,T	0.00	.	AF=0.04;NS=60;SB=-0.42	GT:RD:GQ	0/0:3:1.94	0/0:8:3.42	0/0:1:1.34	0/0:1:1.34	0/0:1:1.04	./.	0/0:2:1.64	0/0:2:1.65	0/0:5:2.54	0/0:6:2.84	0/0:3:1.94	0/0:2:1.64	./.	1/0:4:1.33	0/0:4:2.24	0/0:6:2.85	0/0:6:2.17	0/0:2:1.64	0/0:2:1.64	0/0:2:1.49	0/0:3:1.93	0/0:3:1.94	0/0:4:2.14	./.	0/0:2:1.64	0/0:2:1.36	0/0:2:1.64	0/0:3:1.94	0/0:5:2.55	0/0:4:2.23	0/0:5:2.53	0/0:5:2.54	0/0:1:1.34	0/0:1:1.33	0/0:3:1.94	0/0:1:1.34	0/0:1:1.34	0/0:7:3.15	0/0:2:1.64	0/0:1:1.34	0/0:2:1.64	0/0:1:1.34	0/0:2:1.63	0/0:1:1.34	0/0:4:2.25	1/0:3:1.83	0/0:3:1.38	0/0:2:1.64	0/0:7:3.15	0/2:2:0.58	1/0:6:0.58	0/0:2:0.71	0/0:1:1.32	0/0:4:2.24	0/0:2:1.64	1/0:5:0.98	./.	0/0:3:1.94	0/0:1:1.34	0/0:1:1.34
+1	10000877	.	T	A,C	0.00	.	AF=0.03;NS=60;SB=1.32	GT:RD:GQ	0/0:3:2.14	0/0:7:3.35	0/0:1:1.54	0/0:1:1.54	0/0:1:1.54	0/0:2:1.84	0/0:2:1.84	0/0:2:1.84	0/0:5:2.75	0/0:6:3.03	0/0:3:2.14	0/0:2:1.84	./.	1/0:3:0.77	0/0:4:2.44	0/0:6:3.05	0/0:6:2.86	0/0:3:1.72	0/0:4:2.45	0/0:2:1.84	0/0:3:2.14	0/0:3:2.14	0/0:4:2.20	./.	0/0:2:1.84	0/0:2:1.83	0/0:3:2.14	0/0:3:2.14	0/0:4:2.22	0/0:4:2.44	0/0:5:2.44	0/0:6:3.00	0/0:1:1.54	0/0:1:1.54	0/0:3:2.14	0/0:2:1.84	./.	0/0:7:3.35	0/0:2:1.84	0/0:1:1.54	0/0:2:1.84	0/0:1:1.54	0/0:3:2.14	0/0:1:1.54	0/0:4:2.44	2/0:3:0.90	2/0:4:1.46	0/0:3:1.84	0/0:6:3.05	0/0:2:1.54	2/0:6:0.10	0/0:2:1.83	0/0:1:1.54	0/0:4:2.44	0/0:3:1.84	0/0:5:2.75	./.	0/0:3:2.04	0/0:1:1.54	0/0:1:1.12
+1	10000878	.	C	A	0.00	.	AF=0.03;NS=60;SB=0.59	GT:RD:GQ	0/0:3:2.18	0/0:6:3.07	0/0:1:1.58	0/0:2:1.88	0/0:1:1.58	0/0:2:1.88	0/0:2:1.88	0/0:3:1.88	0/0:5:2.78	0/0:6:2.19	0/0:3:2.17	0/0:2:1.88	./.	0/0:3:1.85	0/0:4:2.48	0/0:5:0.46	0/0:7:2.39	0/0:3:1.84	0/0:4:2.47	0/0:2:1.87	0/0:3:2.17	0/0:3:2.18	0/0:4:2.27	./.	0/0:2:1.88	0/0:2:1.79	0/0:3:2.17	0/0:3:2.18	0/0:4:1.89	0/0:4:2.48	0/0:4:0.49	0/0:6:2.01	0/0:1:1.58	0/0:1:1.13	0/0:3:2.18	0/0:2:1.88	./.	0/0:7:3.38	0/0:3:2.18	0/0:1:1.58	0/0:1:1.56	0/0:1:1.58	0/0:3:2.18	0/0:1:1.58	0/0:4:2.48	0/0:3:2.18	0/0:4:0.09	0/0:3:2.18	0/0:6:3.08	0/0:2:1.87	0/0:6:0.76	0/0:2:0.75	0/0:1:1.58	1/0:4:3.79	0/0:3:2.18	0/0:5:2.48	./.	0/0:3:2.17	0/0:1:1.58	0/0:1:1.30
+1	10000879	.	A	C	0.00	.	AF=0.02;NS=60;SB=0.57	GT:RD:GQ	0/0:3:2.40	0/0:7:3.61	0/0:1:1.80	0/0:2:2.10	0/0:1:1.80	0/0:2:2.10	0/0:2:2.10	0/0:3:2.16	0/0:5:2.97	0/0:6:3.30	0/0:4:2.58	0/0:2:2.10	./.	0/0:3:2.40	0/0:4:2.70	0/0:5:3.00	0/0:7:3.14	0/0:3:2.04	0/0:4:2.70	0/0:4:2.62	0/0:3:2.28	0/0:3:2.40	0/0:4:2.68	./.	0/0:2:2.10	0/0:2:1.77	0/0:3:2.16	0/0:3:2.40	0/0:4:2.52	0/0:4:2.70	0/0:4:2.46	0/0:6:3.30	0/0:1:1.80	0/0:1:1.80	0/0:3:2.35	0/0:2:2.10	./.	0/0:8:3.91	0/0:3:2.40	0/0:1:1.80	0/0:1:1.80	./.	0/0:3:2.40	0/0:1:1.80	0/0:4:2.70	0/0:3:2.40	0/0:4:2.66	0/0:3:2.40	0/0:6:3.30	0/0:2:2.10	0/0:6:0.25	0/0:2:2.10	0/0:1:1.79	0/1:4:3.30	0/0:4:2.68	0/0:5:3.01	./.	0/0:2:2.10	0/0:1:1.80	0/0:1:1.51
+1	10000880	.	A	C	1.18	.	AF=0.01;NS=60;SB=-0.13	GT:RD:GQ	0/0:3:2.83	0/0:7:4.03	0/0:1:2.22	0/0:2:2.52	0/0:1:2.22	0/0:2:2.52	0/0:2:2.52	0/0:3:1.84	0/0:5:3.39	0/0:5:3.42	0/0:4:3.00	./.	./.	0/0:3:2.83	0/0:4:3.13	0/0:5:3.43	0/0:6:3.27	0/0:3:2.71	0/0:4:3.13	0/0:5:3.42	0/0:3:2.70	0/0:3:2.82	0/0:4:3.12	./.	0/0:2:2.52	0/0:3:2.20	0/0:3:2.58	0/0:3:2.83	0/0:4:2.91	0/0:4:3.13	0/0:4:2.88	0/0:6:3.73	0/0:1:2.22	0/0:1:2.22	0/0:3:2.78	0/0:2:2.52	./.	0/0:8:4.33	0/0:4:3.12	0/0:3:2.22	0/0:1:2.22	./.	0/0:3:2.83	0/0:2:2.52	0/0:4:3.13	0/0:3:2.83	0/0:4:3.11	0/0:3:2.82	0/0:6:3.71	0/0:3:2.52	0/0:6:3.73	0/0:3:2.83	0/0:2:2.52	0/0:4:3.13	0/0:4:3.09	0/1:5:0.08	./.	0/0:2:2.52	0/0:1:2.22	0/0:1:2.22
+1	10000887	.	A	T	0.00	.	AF=0.01;NS=60;SB=2.57	GT:RD:GQ	0/0:4:2.72	0/0:8:3.94	0/0:1:1.84	0/0:2:2.14	0/0:1:1.84	0/0:3:2.44	0/0:3:2.21	0/0:4:2.34	0/0:5:3.04	0/0:5:3.04	0/0:4:2.74	0/0:1:1.84	0/0:1:1.84	0/1:4:0.12	0/0:4:2.74	0/0:4:2.74	0/0:8:3.92	0/0:4:2.74	0/0:6:2.87	0/0:7:3.64	0/0:4:2.74	0/0:3:2.43	0/0:5:2.97	0/0:3:2.34	0/0:2:2.14	0/0:5:2.51	0/0:3:2.14	0/0:4:2.26	0/0:3:2.44	0/0:4:2.74	0/0:2:2.14	0/0:6:3.34	0/0:2:2.14	0/0:2:2.14	0/0:4:2.44	0/0:1:1.84	0/0:2:2.14	0/0:8:3.94	0/0:5:3.04	0/0:4:2.74	0/0:2:2.14	0/0:2:2.14	0/0:2:2.14	0/1:3:0.86	0/0:5:3.04	0/0:3:2.44	0/0:5:3.04	0/0:4:2.74	0/0:6:3.34	0/0:7:3.64	0/0:5:3.04	0/0:4:2.44	0/0:5:3.04	0/0:4:2.74	0/0:5:2.94	0/0:5:3.04	0/0:1:1.84	./.	0/0:1:1.84	0/0:2:2.02
+1	10000888	.	A	C	3.94	.	AF=0.01;NS=60;SB=-0.40	GT:RD:GQ	0/0:4:3.00	0/0:8:4.19	0/0:1:2.09	0/0:2:2.39	0/0:1:2.09	0/0:4:2.99	0/0:3:2.69	0/0:4:2.99	0/0:5:3.28	0/0:6:3.59	0/0:4:3.00	0/0:1:2.08	0/0:1:2.09	0/0:4:2.99	0/0:4:3.00	0/0:4:3.00	0/0:9:4.50	0/0:5:2.99	0/0:6:3.53	0/0:8:4.18	0/0:4:2.99	0/0:3:2.68	0/0:5:3.08	0/0:3:2.68	0/0:2:2.39	0/0:6:3.14	0/0:3:2.66	0/0:3:2.68	0/0:3:2.69	0/0:5:3.30	0/0:3:2.39	0/0:6:3.60	0/0:3:2.69	0/0:2:2.39	0/0:4:2.99	0/0:1:1.97	0/0:2:2.39	0/0:8:4.19	0/0:5:2.65	0/0:4:3.00	0/0:2:2.39	0/0:2:2.39	0/0:2:2.39	0/0:3:2.61	0/0:5:3.30	0/0:3:2.69	0/0:6:3.59	0/0:5:2.92	0/0:5:3.30	0/0:7:3.90	0/0:5:3.30	0/0:4:3.00	0/0:5:3.30	0/0:4:3.00	0/0:5:3.29	0/1:5:0.66	0/0:2:2.39	./.	0/0:1:2.09	0/0:2:2.39
+1	10000890	.	T	A	20.18	.	AF=0.07;NS=60;SB=-2.32	GT:RD:GQ	0/0:4:2.05	0/0:8:3.01	0/0:2:1.15	0/0:2:1.46	0/0:1:1.15	0/0:4:2.03	0/0:4:1.76	0/0:4:1.76	0/0:7:0.75	0/0:6:1.89	0/0:6:2.66	0/0:1:1.15	0/0:1:1.15	0/0:4:2.06	1/0:4:1.11	1/0:3:1.40	0/0:8:3.25	0/0:5:2.36	1/0:6:0.64	0/0:8:3.25	0/0:4:1.33	1/0:3:0.67	0/0:5:2.05	0/0:3:1.75	1/0:2:1.91	0/0:6:2.66	0/0:2:1.45	0/0:3:1.74	0/0:3:1.31	0/0:5:2.35	0/0:4:2.06	0/0:6:1.09	0/0:3:1.72	0/0:2:1.46	0/0:4:1.59	0/0:2:0.90	0/0:2:1.46	0/0:8:3.08	0/0:5:0.30	0/0:4:2.06	0/0:2:1.46	0/0:2:1.46	0/0:1:1.15	0/0:3:1.75	0/0:5:2.36	0/0:2:1.45	0/0:6:2.39	0/0:5:2.35	0/0:4:2.03	0/0:7:2.88	1/0:5:0.80	0/0:5:2.36	0/0:5:2.36	0/0:3:1.75	0/0:5:0.37	0/0:5:2.06	0/0:2:1.45	./.	0/0:1:1.15	0/0:2:1.45
+1	10000897	.	T	A	2.52	.	AF=0.01;NS=60;SB=-0.26	GT:RD:GQ	0/0:6:3.65	0/0:9:4.54	0/0:2:2.31	0/0:3:1.87	0/0:2:2.15	0/0:4:2.64	0/0:5:3.21	0/0:3:2.75	0/0:7:3.92	0/0:7:3.75	0/0:6:3.26	0/0:1:2.15	0/0:1:2.13	0/0:4:3.05	0/0:4:3.05	0/0:3:2.75	0/0:11:3.95	0/0:4:2.82	0/0:6:3.65	0/0:9:4.55	0/0:4:2.80	0/0:3:2.41	0/0:4:2.83	0/0:4:2.99	0/0:2:2.45	0/0:7:3.88	1/0:3:0.41	0/0:5:0.94	0/0:2:2.45	0/0:6:3.65	0/0:5:3.04	0/0:6:3.15	0/0:2:2.45	0/0:2:2.45	0/0:6:3.00	0/0:2:2.04	0/0:2:2.45	0/0:9:4.49	0/0:5:3.34	0/0:4:3.05	0/0:2:2.44	0/0:2:2.45	0/0:2:2.44	0/0:4:2.48	0/0:5:3.35	0/0:3:2.75	0/0:6:3.40	0/0:7:3.95	0/0:3:2.75	0/0:10:4.74	0/0:4:3.05	0/0:7:3.73	0/0:7:3.95	0/0:3:2.75	0/0:5:3.05	0/0:5:3.35	0/0:3:2.61	./.	0/0:1:2.14	0/0:4:2.74
+1	10000900	.	G	A	0.00	.	AF=0.02;NS=60;SB=2.49	GT:RD:GQ	0/0:5:2.93	0/0:9:1.47	0/0:3:2.31	1/0:2:0.72	0/0:1:1.73	0/0:4:2.63	0/0:4:2.63	0/0:3:2.33	0/0:6:3.23	0/0:6:3.20	0/0:7:3.25	0/0:2:2.03	0/0:1:1.73	0/0:3:2.33	0/0:3:2.33	0/0:3:2.33	0/0:9:4.13	0/0:3:2.02	0/0:6:2.85	0/0:9:3.10	0/0:4:2.62	0/0:2:0.64	0/0:4:2.39	0/0:4:2.31	0/0:2:2.03	0/0:7:3.53	0/0:5:2.03	0/0:6:3.17	0/0:1:1.73	0/0:6:3.22	0/0:5:2.92	0/0:6:3.21	0/0:2:2.03	0/0:2:2.03	0/0:5:2.93	0/0:1:1.73	0/0:2:2.03	0/0:9:4.13	1/0:5:0.67	0/0:4:2.63	0/0:4:2.63	0/0:2:2.03	0/0:2:2.03	0/0:6:1.75	0/0:7:3.53	0/0:3:2.33	0/0:6:3.22	0/0:7:3.53	0/0:2:2.03	0/0:9:4.13	0/0:4:2.63	0/0:7:3.47	0/0:6:3.23	0/0:3:2.33	0/0:5:2.93	0/0:4:2.63	0/0:3:2.33	0/0:1:1.43	0/0:1:1.73	0/0:3:2.33
+1	10000901	.	A	G	4.04	.	AF=0.01;NS=60;SB=-0.41	GT:RD:GQ	0/0:4:3.00	0/0:9:4.50	0/0:3:2.70	0/0:2:2.40	0/0:1:2.10	0/0:4:3.00	0/0:4:3.00	0/0:3:2.70	0/0:7:3.91	0/0:6:3.59	0/0:7:3.84	0/0:2:2.38	0/0:1:2.10	0/0:3:2.70	0/0:3:2.70	0/0:3:2.70	0/0:11:4.50	0/0:3:2.69	0/0:6:3.59	0/0:9:4.27	0/0:4:3.00	0/0:2:2.40	0/0:4:2.57	0/0:4:3.00	0/0:2:2.40	0/0:7:3.91	0/0:5:3.28	0/0:7:3.37	0/0:1:2.10	0/0:6:3.60	0/0:5:3.27	0/0:6:3.61	0/0:2:2.40	0/0:2:2.40	0/0:4:3.00	0/0:1:2.10	0/0:2:2.40	0/0:9:4.50	0/1:5:0.68	0/0:4:3.00	0/0:4:3.00	0/0:2:2.40	0/0:2:2.40	0/0:6:3.58	0/0:7:3.91	0/0:3:2.70	0/0:6:3.60	0/0:8:3.91	0/0:2:2.40	0/0:9:4.21	0/0:4:3.00	0/0:7:3.78	0/0:6:3.61	0/0:3:2.70	0/0:7:3.30	0/0:4:3.00	0/0:3:2.70	0/0:1:2.10	0/0:1:2.10	0/0:5:2.69
+1	10000906	.	G	A	1.16	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:5:2.00	0/0:9:4.28	0/0:8:4.02	0/0:3:2.81	0/0:1:2.26	0/0:5:3.13	0/0:3:2.56	0/0:2:2.56	0/0:8:4.34	0/0:6:3.71	0/0:8:4.06	0/0:2:2.55	0/0:1:2.26	0/0:3:2.86	0/0:3:2.86	0/0:2:2.56	0/0:12:4.95	0/0:5:3.45	0/0:6:3.74	0/0:9:4.65	0/0:4:3.15	0/0:1:2.26	0/0:4:3.13	0/0:5:3.16	0/0:2:2.56	0/0:7:3.76	0/0:5:1.23	0/0:8:3.96	0/0:2:2.26	0/0:7:4.06	0/0:4:3.13	0/0:9:4.31	0/0:3:2.52	0/0:2:2.56	0/0:5:3.32	0/0:1:2.26	0/0:2:2.56	0/0:9:4.64	1/0:5:0.06	0/0:2:2.56	0/0:3:2.86	0/0:2:2.56	0/0:4:2.32	0/0:7:3.92	0/0:7:4.06	0/0:3:2.86	0/0:6:3.75	0/0:7:4.06	0/0:2:2.56	0/0:7:4.04	0/0:4:3.16	0/0:8:3.20	0/0:7:3.76	0/0:3:2.86	0/0:7:4.02	0/0:4:3.16	0/0:3:2.86	0/0:1:2.26	0/0:1:2.25	0/0:6:3.73
+1	10000915	.	G	C	1.71	.	AF=0.01;NS=60;SB=-2.10	GT:RD:GQ	0/0:5:3.44	0/0:11:5.01	0/0:6:3.73	0/0:4:3.02	0/0:5:3.44	0/0:6:3.74	0/0:2:2.51	./.	0/0:8:4.33	0/0:5:3.44	0/0:9:4.64	0/0:4:3.13	0/0:1:2.23	0/0:3:2.83	0/0:3:2.83	0/0:1:2.23	0/0:10:4.94	0/0:4:2.83	0/0:6:3.69	0/0:8:4.32	0/0:5:3.44	0/0:2:2.14	0/0:8:4.04	0/0:3:2.83	0/0:3:2.83	0/0:8:4.03	0/0:6:2.67	0/0:8:4.04	0/0:8:4.34	0/0:7:4.04	0/0:4:3.13	0/0:10:3.06	0/0:3:2.83	0/0:1:2.23	0/0:4:3.13	0/0:2:2.53	0/0:1:2.23	0/0:8:3.61	0/0:5:3.13	0/0:3:1.49	0/0:3:2.83	0/0:4:3.13	0/0:5:2.01	1/0:8:0.24	0/0:6:3.73	0/0:3:2.83	0/0:6:3.73	0/0:6:3.35	0/0:1:2.23	0/0:7:4.04	0/0:5:3.44	0/0:5:3.23	0/0:6:3.74	0/0:3:2.83	0/0:6:3.74	0/0:4:3.13	0/0:2:2.53	0/0:1:2.23	0/0:2:2.53	0/0:6:3.74
+1	10000935	.	C	A	5.17	.	AF=0.01;NS=60;SB=-0.52	GT:RD:GQ	0/0:4:2.95	0/0:8:4.13	0/0:7:3.86	0/0:5:3.26	0/0:6:2.36	0/0:6:3.52	0/0:3:2.66	0/0:3:2.66	0/0:5:3.21	0/0:3:2.66	0/0:15:5.96	0/0:4:2.96	0/0:2:2.35	0/0:3:2.66	0/0:4:2.96	0/0:1:2.05	0/0:11:4.46	0/0:6:3.26	0/0:3:2.66	0/0:5:3.26	0/0:4:2.66	0/0:2:2.36	0/0:5:3.26	0/0:3:2.66	0/0:3:2.66	0/0:9:4.32	0/0:8:4.11	0/0:6:3.56	0/0:12:4.75	0/0:4:2.96	0/0:18:6.85	0/0:8:4.16	0/0:2:2.36	./.	0/0:2:2.35	0/0:5:3.25	./.	0/0:8:4.16	0/0:6:3.56	0/0:5:3.26	0/0:5:3.26	0/0:4:2.96	0/0:8:4.16	0/0:5:3.25	0/0:6:3.56	0/0:1:2.05	0/0:5:1.63	0/0:8:4.16	0/0:1:2.05	0/0:3:2.63	0/0:5:3.26	1/0:4:0.84	0/0:3:2.66	0/0:3:2.66	0/0:5:3.25	0/0:6:3.56	0/0:1:2.05	./.	0/0:4:2.96	0/0:1:2.05
+1	10000964	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.23	GT:RD:GQ	0/0:3:2.61	0/0:7:3.84	0/0:3:2.33	0/0:3:2.63	0/0:3:2.63	0/0:10:4.71	0/0:1:2.03	0/0:3:2.63	1/0:3:1.16	0/0:5:3.23	0/0:14:5.94	./.	0/0:2:2.31	0/0:3:2.63	0/0:4:2.93	0/0:1:2.03	0/0:8:4.13	0/0:2:2.33	0/0:4:2.93	0/0:5:3.23	0/0:4:2.93	0/0:3:2.63	0/0:3:2.63	0/0:3:2.63	0/0:3:2.63	0/0:4:2.93	0/0:4:2.92	0/0:8:4.14	0/0:9:4.43	0/0:5:3.23	0/0:7:3.84	0/0:2:2.33	0/0:3:2.63	0/0:1:2.03	0/0:4:2.93	0/0:1:2.03	0/0:2:2.25	0/0:7:3.83	0/0:6:3.53	0/0:5:3.23	0/0:7:3.83	0/0:4:2.93	0/0:6:3.53	0/0:3:2.63	0/0:5:3.23	0/0:2:2.33	0/0:2:2.33	0/0:6:3.41	0/0:4:2.93	0/0:3:2.63	0/0:6:3.53	0/0:6:3.53	0/0:3:2.63	0/0:3:2.63	0/0:2:2.33	0/0:7:3.83	0/0:1:1.97	0/0:2:2.33	0/0:3:2.62	./.
+1	10000978	.	G	A	3.17	.	AF=0.01;NS=60;SB=-0.33	GT:RD:GQ	0/0:4:2.86	0/0:7:3.87	0/0:2:2.39	0/0:3:2.63	0/0:2:2.09	0/0:8:4.19	0/0:3:2.69	0/0:1:1.79	0/0:5:3.29	0/0:5:3.29	0/0:15:5.98	0/0:4:2.99	0/0:1:2.09	0/0:2:2.38	0/0:4:2.99	0/0:1:2.09	0/0:5:2.99	0/0:1:2.09	0/0:3:2.69	0/0:4:2.99	0/0:3:2.65	0/0:2:2.38	0/0:2:2.39	0/0:1:2.09	0/0:2:2.39	0/0:4:2.69	1/0:4:0.54	0/0:5:3.29	0/0:4:2.64	0/0:5:3.29	0/0:6:3.59	0/0:3:2.69	0/0:3:2.69	0/0:1:2.09	0/0:9:4.19	0/0:1:2.09	0/0:2:2.32	0/0:7:3.89	0/0:6:3.59	0/0:3:2.69	0/0:7:3.89	0/0:3:2.69	0/0:7:3.85	0/0:2:2.39	0/0:4:2.99	0/0:1:2.09	0/0:1:2.09	0/0:2:2.34	0/0:6:3.57	0/0:5:3.27	0/0:5:3.29	0/0:4:2.99	0/0:8:3.81	0/0:2:2.39	0/0:4:2.92	0/0:7:3.88	./.	./.	0/0:3:2.69	0/0:1:2.09
+1	10000995	.	T	A,C	5.02	.	AF=0.01;NS=60;SB=-2.85	GT:RD:GQ	0/0:5:3.31	1/0:4:0.43	0/0:4:2.64	0/0:5:3.31	0/0:2:2.18	0/0:4:3.01	0/0:3:2.60	./.	0/0:4:3.01	0/0:4:3.00	0/0:13:5.71	0/0:4:3.01	0/0:2:2.41	0/0:2:2.41	0/0:4:3.01	0/0:2:2.41	0/0:7:3.89	0/0:4:2.71	0/0:4:2.61	0/0:5:3.30	0/0:5:3.31	0/0:1:2.11	0/0:4:2.98	./.	0/0:3:2.71	0/0:8:4.22	0/0:3:2.67	0/0:4:3.01	0/0:5:3.08	0/0:6:3.61	0/0:7:3.91	0/0:4:3.01	0/0:1:2.11	0/0:1:2.11	0/0:9:4.52	./.	0/0:1:2.11	0/0:8:4.22	0/0:6:3.61	0/0:2:2.41	0/0:8:4.22	0/0:3:2.71	0/0:5:3.28	0/0:1:2.11	0/0:6:3.60	0/0:2:2.41	0/0:1:2.11	0/0:2:2.41	0/0:6:3.60	0/0:3:2.70	0/0:5:3.31	./.	0/0:8:4.16	2/0:2:0.43	0/0:6:3.61	0/0:7:3.91	0/0:1:2.11	0/0:1:1.81	0/0:3:2.71	0/0:5:3.31
+1	10000996	.	G	T	1.71	.	AF=0.01;NS=60;SB=-0.18	GT:RD:GQ	0/0:5:3.40	0/0:4:3.09	0/0:4:3.09	0/0:5:3.40	0/0:2:2.22	0/0:4:3.10	0/0:4:2.80	./.	0/0:4:3.10	0/0:4:3.08	0/0:13:5.80	0/0:4:3.10	0/0:2:2.50	0/0:2:2.50	0/0:4:3.10	0/0:2:2.50	0/0:7:3.45	0/0:3:2.78	0/1:4:0.24	0/0:5:3.40	0/0:5:3.37	0/0:1:2.20	0/0:4:3.08	./.	0/0:3:2.80	0/0:8:4.31	0/0:3:2.73	0/0:5:3.40	0/0:5:3.12	0/0:6:3.70	0/0:7:4.00	0/0:4:3.10	0/0:1:2.20	0/0:1:2.20	0/0:9:4.46	0/0:1:2.20	0/0:1:2.20	0/0:8:4.31	0/0:6:3.70	0/0:2:2.50	0/0:7:4.00	0/0:2:2.50	0/0:5:2.80	0/0:1:2.19	0/0:6:3.68	0/0:2:2.50	0/0:1:2.20	0/0:2:2.50	0/0:6:3.70	0/0:3:2.79	0/0:5:3.40	./.	0/0:7:3.99	0/0:2:2.50	0/0:6:3.70	0/0:7:4.00	0/0:2:2.45	0/0:1:2.20	0/0:3:2.80	0/0:5:3.40

public/testdata/NA12878.chr1_10mb_11mb.slx.indels.vcf4

@@ -0,0 +1,5 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+1	10075180	.	G	GAAAAG	.	PASS	.	GT	1/0
+1	10093647	.	CTCT	C	.	PASS	.	GT	1/0
+1	10271352	.	G	GTTTT	.	PASS	.	GT	1/0

public/testdata/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf

@@ -0,0 +1,243 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=ABFilter,Description="AB  0.75 && DP  40">
+##FILTER=<ID=DPFilter,Description="DP  120 || SB  -0.10">
+##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
+##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
+##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
+##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual  0.06">
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP))  0.1)">
+##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FilterLiftedVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/tmp/0.069557317373441.sorted.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=FilterLiftedVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##LiftoverVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/home/radon01/kiran/scr1/projects/DataProcessingPaper/results/newForStacey/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=LiftoverVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub chain=/humgen/gsa-hpprojects/GATK/data/Liftover_Chain_Files/hg18ToHg19.broad.over.chain newSequenceDictionary=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dict"
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:10000000-10100000] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false"
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,chrX] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
+##source=SelectVariants
+##source=VariantOptimizer
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	10000117	rs4816203	C	T	77.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=867.45;QD=13.77;SB=-268.09	GT:AD:DP:GL:GQ	0/1:36,27:63:-109.01,-18.98,-129.63:99
+20	10000211	rs4813908	C	T	273.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.66;MQ0=0;OQ=913.43;QD=16.61;SB=-383.86	GT:AD:DP:GL:GQ	0/1:28,27:53:-110.59,-15.96,-95.89:99
+20	10000439	rs4816204	T	G	489.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2354.98;QD=29.44;SB=-1083.04	GT:AD:DP:GL:GQ	1/1:0,80:77:-239.15,-23.21,-0.06:99
+20	10000598	rs6057087	T	A	659.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=1772.11;QD=36.92;SB=-761.69	GT:AD:DP:GL:GQ	1/1:0,48:48:-180.81,-14.46,-0.01:99
+20	10000694	rs6057088	G	A	276.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=49.18;MQ0=0;OQ=1128.96;QD=14.11;SB=-510.63	GT:AD:DP:GL:GQ	0/1:46,34:80:-140.27,-24.09,-169.48:99
+20	10000758	rs6057089	T	A	243.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.23;MQ0=0;OQ=3541.99;QD=38.92;SB=-1671.36	GT:AD:DP:GL:GQ	1/1:0,91:91:-353.20,-27.40,-0.02:99
+20	10001019	rs6077626	T	G	401.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.70;MQ0=2;OQ=712.45;QD=10.33;SB=-352.52	GT:AD:DP:GL:GQ	0/1:40,29:65:-94.10,-19.57,-146.27:99
+20	10001298	rs1535165	T	A	637.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.34;MQ0=0;OQ=2708.88;QD=36.61;SB=-1143.40	GT:AD:DP:GL:GQ	1/1:0,73:73:-274.49,-21.99,-0.02:99
+20	10001474	rs1535166	C	T	608.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.97;MQ0=0;OQ=2678.14;QD=38.26;SB=-1011.68	GT:AD:DP:GL:GQ	1/1:0,70:69:-271.42,-20.79,-0.02:99
+20	10001617	rs2876191	C	A	279.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.17;MQ0=0;OQ=1439.09;QD=14.25;SB=-481.71	GT:AD:DP:GL:GQ	0/1:52,49:101:-177.61,-30.42,-186.45:99
+20	10001628	rs1535167	G	A	101.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.36;MQ0=0;OQ=3780.26;QD=40.22;SB=-1550.04	GT:AD:DP:GL:GQ	1/1:0,93:93:-377.03,-30.13,-2.37:99
+20	10001661	rs1535168	T	C	621.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=2787.58;QD=34.41;SB=-1177.74	GT:AD:DP:GL:GQ	1/1:0,81:79:-282.37,-23.79,-0.02:99
+20	10001670	rs1535169	T	G	512.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.21;MQ0=0;OQ=2852.67;QD=35.22;SB=-1272.32	GT:AD:DP:GL:GQ	1/1:0,81:80:-288.87,-24.09,-0.02:99
+20	10002058	rs4404352	T	G	305.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.60;MQ0=0;OQ=2628.53;QD=34.14;SB=-934.22	GT:AD:DP:GL:GQ	1/1:1,76:75:-266.46,-22.59,-0.03:99
+20	10002099	rs4555427	C	T	2.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=5;HaplotypeScore=0.47;MQ=56.02;MQ0=0;OQ=1117.99;QD=17.47;SB=-498.13	GT:AD:DP:GL:GQ	0/1:27,37:61:-133.46,-18.38,-95.58:99
+20	10002138	rs4569544	C	G	481.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.30;MQ0=0;OQ=2204.77;QD=40.09;SB=-1043.64	GT:AD:DP:GL:GQ	1/1:0,55:51:-224.08,-15.37,-0.01:99
+20	10002142	rs4417777	G	C	579.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=2117.84;QD=39.22;SB=-975.74	GT:AD:DP:GL:GQ	1/1:0,54:49:-215.38,-14.76,-0.01:99
+20	10002470	rs2327260	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=11;HaplotypeScore=1.75;MQ=47.38;MQ0=0;OQ=2328.93;QD=34.25;SB=-1076.99	GT:AD:DP:GL:GQ	1/1:0,68:61:-236.50,-18.38,-0.02:99
+20	10002478	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=7;HaplotypeScore=9.60;MQ=53.59;MQ0=0;OQ=111.85;QD=2.00;SB=59.21	GT:AD:DP:GL:GQ	0/1:47,9:46:-28.33,-13.86,-140.18:99
+20	10002625	rs2144570	G	T	624.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=2238.72;QD=36.11;SB=-983.67	GT:AD:DP:GL:GQ	1/1:0,62:61:-227.47,-18.37,-0.01:99
+20	10003021	rs6057090	C	T	599.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2357.20;QD=38.64;SB=-1005.68	GT:AD:DP:GL:GQ	1/1:0,61:60:-239.32,-18.08,-0.02:99
+20	10003358	rs926982	A	C	283.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1239.40;QD=14.58;SB=-411.81	GT:AD:DP:GL:GQ	0/1:43,42:84:-152.52,-25.30,-151.13:99
+20	10003651	rs926984	T	C	632.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=3208.86;QD=35.65;SB=-1068.08	GT:AD:DP:GL:GQ	1/1:0,90:89:-324.50,-26.81,-0.03:99
+20	10003692	rs2064653	A	G	614.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=2247.29;QD=34.05;SB=-940.96	GT:AD:DP:GL:GQ	1/1:0,66:65:-228.34,-19.58,-0.03:99
+20	10003832	rs6057091	G	A	453.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=2581.24;QD=40.33;SB=-971.37	GT:AD:DP:GL:GQ	1/1:0,64:64:-261.72,-19.28,-0.01:99
+20	10004094	rs1988590	A	C	5.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=53.93;MQ0=0;OQ=1571.64;QD=30.82;SB=-600.05	GT:AD:DP:GL:GQ	1/1:0,51:46:-160.77,-13.86,-0.02:99
+20	10004147	rs1988591	A	G	22.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.77;MQ=56.98;MQ0=0;OQ=1621.26;QD=30.59;SB=-586.00	GT:AD:DP:GL:GQ	1/1:0,53:50:-165.75,-15.08,-0.04:99
+20	10004193	.	G	T	112	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.87;MQ0=0;OQ=817.22;QD=15.13;SB=-391.14	GT:AD:DP:GL:GQ	0/1:25,29:51:-100.37,-15.36,-82.85:99
+20	10004351	rs6057092	C	G	541.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2906.33;QD=42.74;SB=-1364.94	GT:AD:DP:GL:GQ	1/1:0,68:67:-294.24,-20.19,-0.02:99
+20	10004389	rs6057093	T	G	609.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.09;MQ0=0;OQ=2210.27;QD=35.65;SB=-884.11	GT:AD:DP:GL:GQ	1/1:0,62:62:-224.63,-18.68,-0.02:99
+20	10004610	rs2064654	A	C	2.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=10.08;MQ=58.45;MQ0=0;OQ=3199.99;QD=35.56;SB=-1545.20	GT:AD:DP:GL:GQ	1/1:1,89:88:-323.60,-26.50,-0.02:99
+20	10004725	rs10485737	A	G	457.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.27;MQ0=0;OQ=850.43;QD=13.08;SB=-367.17	GT:AD:DP:GL:GQ	0/1:35,30:65:-107.90,-19.58,-141.57:99
+20	10004874	rs725567	A	C	315.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.30;MQ0=0;OQ=2956.73;QD=35.20;SB=-1190.16	GT:AD:DP:GL:GQ	1/1:0,84:83:-299.28,-25.00,-0.02:99
+20	10004887	rs725566	A	G	256.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.44;MQ0=0;OQ=1129.32;QD=13.61;SB=-455.56	GT:AD:DP:GL:GQ	0/1:44,39:82:-140.92,-24.70,-171.36:99
+20	10005010	rs725565	C	T	706.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2824.42;QD=39.23;SB=-1089.38	GT:AD:DP:GL:GQ	1/1:0,72:71:-286.04,-21.39,-0.02:99
+20	10005427	rs6057094	C	T	587.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2155.03;QD=39.91;SB=-1081.37	GT:AD:DP:GL:GQ	1/1:0,54:54:-219.10,-16.26,-0.01:99
+20	10005499	rs6077631	A	G	634.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2607.55;QD=35.72;SB=-1078.12	GT:AD:DP:GL:GQ	1/1:0,73:73:-264.36,-21.99,-0.02:99
+20	10005587	rs6108375	A	G	498.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1061.48;QD=14.95;SB=-522.04	GT:AD:DP:GL:GQ	0/1:35,36:70:-130.52,-21.08,-138.09:99
+20	10005723	rs6108376	A	G	529.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2687.35;QD=31.62;SB=-1283.54	GT:AD:DP:GL:GQ	1/1:0,85:83:-272.38,-25.03,-0.06:99
+20	10006291	rs6118856	G	A	172.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=908.18;QD=11.08;SB=-459.38	GT:AD:DP:GL:GQ	0/1:53,29:82:-118.80,-24.70,-191.13:99
+20	10006404	rs926985	A	C	490.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2586.62;QD=33.59;SB=-921.26	GT:AD:DP:GL:GQ	1/1:0,77:75:-262.28,-22.59,-0.03:99
+20	10006682	rs6057095	T	A	131.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.43;MQ0=0;OQ=2662.92;QD=36.48;SB=-986.49	GT:AD:DP:GL:GQ	1/1:0,72:71:-269.90,-21.39,-0.02:99
+20	10007150	rs11904989	G	C	276.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.70;MQ0=0;OQ=742.20;QD=11.78;SB=-296.80	GT:AD:DP:GL:GQ	0/1:38,25:60:-95.59,-18.09,-157.44:99
+20	10007175	rs2207850	C	T	90.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.69;MQ0=0;OQ=1294.38;QD=21.22;SB=-604.18	GT:AD:DP:GL:GQ	0/1:22,39:58:-150.19,-17.47,-75.88:99
+20	10007352	rs1884399	C	T	614.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2708.19;QD=39.25;SB=-1162.02	GT:AD:DP:GL:GQ	1/1:0,69:68:-274.43,-20.49,-0.02:99
+20	10007531	rs1884400	A	G	493.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2611.60;QD=36.78;SB=-843.33	GT:AD:DP:GL:GQ	1/1:0,71:71:-264.76,-21.38,-0.02:99
+20	10007980	rs2876192	A	C	668.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.73;MQ0=0;OQ=3022.49;QD=34.35;SB=-1434.18	GT:AD:DP:GL:GQ	1/1:0,88:87:-305.86,-26.20,-0.03:99
+20	10008221	rs2876193	T	C	510.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.18;MQ0=0;OQ=2840.34;QD=36.41;SB=-1397.57	GT:AD:DP:GL:GQ	1/1:0,78:78:-287.64,-23.49,-0.02:99
+20	10008458	rs6087107	T	G	157.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=52.94;MQ0=0;OQ=2398.43;QD=33.78;SB=-1015.12	GT:AD:DP:GL:GQ	1/1:0,71:68:-243.45,-20.48,-0.02:99
+20	10008742	rs12479925	G	T	146.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=35.86;MQ0=1;OQ=685.54;QD=12.24;SB=-274.47	GT:AD:DP:GL:GQ	0/1:26,30:43:-84.79,-12.96,-61.80:99
+20	10008951	.	A	C	553.29	Indel	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=16.13;MQ=51.15;MQ0=0;QD=11.77;SB=-184.92	GT:AD:DP:GL:GQ	0/1:23,24:43:-71.58,-12.97,-70.23:99
+20	10009227	rs12481420	A	G	523.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1201.44;QD=19.70;SB=-625.90	GT:AD:DP:GL:GQ	0/1:22,39:61:-141.80,-18.37,-90.52:99
+20	10009246	rs4574174	A	G	634.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=2711.91;QD=35.68;SB=-1179.49	GT:AD:DP:GL:GQ	1/1:0,76:75:-274.80,-22.59,-0.02:99
+20	10009400	rs6057096	T	A	7.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2788.17;QD=38.19;SB=-1314.62	GT:AD:DP:GL:GQ	1/1:0,73:73:-282.42,-21.98,-0.01:99
+20	10009512	rs6039657	C	G	565.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=3160.94;QD=41.59;SB=-1228.86	GT:AD:DP:GL:GQ	1/1:0,76:74:-319.70,-22.30,-0.02:99
+20	10009719	rs6057097	A	G	58.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.33;MQ0=0;OQ=1551.35;QD=25.02;SB=-585.82	GT:AD:DP:GL:GQ	1/1:0,62:50:-158.78,-15.09,-0.06:99
+20	10009795	rs6118861	A	G	501.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1594.00;QD=35.42;SB=-578.40	GT:AD:DP:GL:GQ	1/1:0,45:45:-163.00,-13.55,-0.01:99
+20	10009844	rs6057098	G	A	11.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.92;MQ=52.80;MQ0=0;OQ=1658.97;QD=30.16;SB=-750.39	GT:AD:DP:GL:GQ	0/1:8,47:51:-184.54,-15.37,-17.54:21.74
+20	10009871	rs6133780	A	G	1067.52	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=16.85;MQ=51.54;MQ0=0;QD=18.09;SB=-387.29	GT:AD:DP:GL:GQ	0/1:19,40:49:-124.80,-14.77,-52.03:99
+20	10009875	rs6133781	A	G	1106.95	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=19.06;MQ=51.21;MQ0=0;QD=19.42;SB=-410.34	GT:AD:DP:GL:GQ	0/1:16,41:44:-127.23,-13.25,-35.68:99
+20	10009879	.	A	G	1218.05	SnpCluster	AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;HRun=1;HaplotypeScore=20.77;MQ=51.40;MQ0=0;QD=23.88;SB=-543.65	GT:AD:DP:GL:GQ	1/1:5,46:42:-136.91,-12.65,-11.59:10.59
+20	10009883	rs6133782	A	G	1399.75	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=11.88;MQ=52.16;MQ0=0;QD=27.45;SB=-484.45	GT:AD:DP:GL:GQ	1/1:2,49:43:-147.73,-12.95,-4.17:87.80
+20	10010393	rs513998	T	G	602.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=1247.20;QD=16.20;SB=-518.70	GT:AD:DP:GL:GQ	0/1:35,42:76:-150.89,-22.89,-128.62:99
+20	10010766	rs517531	T	G	421.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2100.93;QD=31.36;SB=-978.12	GT:AD:DP:GL:GQ	1/1:0,66:67:-217.39,-23.46,-3.72:99
+20	10010832	rs582827	T	C	733.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=2668.46;QD=35.58;SB=-1048.08	GT:AD:DP:GL:GQ	1/1:0,75:75:-270.45,-22.59,-0.02:99
+20	10011075	rs6039659	C	T	234.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=1322.11;QD=15.74;SB=-644.72	GT:AD:DP:GL:GQ	0/1:45,39:82:-160.20,-24.71,-141.60:99
+20	10011309	rs641722	T	C	546.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2396.22;QD=30.72;SB=-1026.41	GT:AD:DP:GL:GQ	1/1:0,78:76:-243.28,-22.92,-0.07:99
+20	10011666	rs546821	C	T	285.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2849.79;QD=40.14;SB=-1187.35	GT:AD:DP:GL:GQ	1/1:0,71:71:-288.58,-21.39,-0.02:99
+20	10011939	rs548863	C	T	181.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=56.14;MQ0=0;OQ=2488.04;QD=39.49;SB=-885.19	GT:AD:DP:GL:GQ	1/1:0,63:62:-252.40,-18.68,-0.01:99
+20	10012362	rs574425	G	T	17.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=51.41;MQ0=0;OQ=676.99;QD=28.21;SB=-89.90	GT:AD:DP:GL:GQ	1/1:0,24:20:-71.29,-6.02,-0.01:60.18
+20	10012384	rs7270107	T	C	128.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=51.62;MQ0=0;OQ=216.13;QD=12.01;SB=-75.35	GT:AD:DP:GL:GQ	0/1:9,9:16:-29.72,-4.82,-34.04:99
+20	10012387	rs6057102	T	C	18.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=50.47;MQ0=0;OQ=295.02;QD=18.44;SB=-77.36	GT:AD:DP:GL:GQ	1/1:0,16:11:-33.10,-3.32,-0.02:33.06
+20	10012479	rs575394	A	G	3.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=49.52;MQ0=0;OQ=474.16;QD=23.71;SB=-247.57	GT:AD:DP:GL:GQ	1/1:0,20:16:-51.02,-4.83,-0.02:48.10
+20	10012498	rs657453	C	G	2.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=40.06;MQ0=0;OQ=331.25;QD=22.08;SB=-84.82	GT:AD:DP:GL:GQ	1/1:0,15:9:-36.71,-2.71,-0.01:27.09
+20	10012518	rs657490	T	C	1.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.64;MQ=34.32;MQ0=0;OQ=366.95;QD=22.93;SB=-197.06	GT:AD:DP:GL:GQ	1/1:0,16:12:-40.29,-3.62,-0.01:36.09
+20	10012521	rs6141099	C	T	33.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=35.97;MQ0=0;OQ=104.02;QD=5.78;SB=-64.27	GT:AD:DP:GL:GQ	0/1:11,7:14:-17.91,-4.23,-28.63:99
+20	10012636	rs57357029	G	C	442.35	Indel	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=46.22;MQ0=1;QD=17.69;SB=-127.71	GT:AD:DP:GL:GQ	0/1:10,15:20:-53.56,-6.04,-26.16:99
+20	10012714	rs577258	G	C	4.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=54.18;MQ0=0;OQ=1374.69;QD=38.19;SB=-268.50	GT:AD:DP:GL:GQ	1/1:0,36:34:-141.07,-10.25,-0.02:99
+20	10012751	rs577383	T	C	3.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=51.17;MQ0=0;OQ=807.71;QD=26.06;SB=-389.47	GT:AD:DP:GL:GQ	1/1:0,31:26:-84.38,-7.84,-0.03:78.14
+20	10013119	rs670350	C	T	14.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=53.67;MQ0=0;OQ=1037.37;QD=17.58;SB=-503.12	GT:AD:DP:GL:GQ	0/1:27,32:57:-124.19,-17.17,-93.21:99
+20	10013574	rs6057108	G	A	190.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.43;MQ0=0;OQ=995.08;QD=15.08;SB=-284.14	GT:AD:DP:GL:GQ	0/1:36,30:66:-122.67,-19.88,-129.26:99
+20	10015679	.	C	T	4.66	PASS	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=130.84;QD=11.89;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,6:10:-19.38,-3.01,-17.14:99
+20	10015761	rs12106014	T	C	188.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=282.39;QD=12.84;SB=-35.94	GT:AD:DP:GL:GQ	0/1:9,13:21:-37.85,-6.33,-34.21:99
+20	10018158	rs512313	G	C	152.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.79;MQ0=0;OQ=1786.48;QD=20.53;SB=-749.98	GT:AD:DP:GL:GQ	0/1:39,47:85:-207.56,-25.63,-151.93:99
+20	10018555	rs570855	G	A	501.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1507.16;QD=18.61;SB=-748.62	GT:AD:DP:GL:GQ	0/1:36,45:80:-178.09,-24.09,-134.36:99
+20	10019093	rs575534	A	G	198.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.34;MQ0=0;OQ=1097.34;QD=15.68;SB=-511.28	GT:AD:DP:GL:GQ	0/1:34,36:69:-133.80,-20.78,-132.32:99
+20	10020229	rs596203	G	A	334.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.76;MQ0=0;OQ=1448.48;QD=18.34;SB=-632.66	GT:AD:DP:GL:GQ	0/1:37,42:79:-171.94,-23.81,-120.12:99
+20	10023689	rs4813909	G	A	153.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.04;MQ0=0;OQ=1887.80;QD=22.74;SB=-948.03	GT:AD:DP:GL:GQ	0/1:30,53:83:-217.06,-25.00,-110.51:99
+20	10024107	.	C	T	114.08	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.56;MQ0=0;OQ=1618.74;QD=19.04;SB=-735.06	GT:AD:DP:GL:GQ	0/1:38,47:84:-190.47,-25.31,-121.49:99
+20	10024288	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=5;HaplotypeScore=7.93;MQ=51.94;MQ0=0;OQ=68.97;QD=0.97;SB=86.23	GT:AD:DP:GL:GQ	0/1:53,18:57:-27.36,-17.18,-167.04:99
+20	10024294	.	C	T	19.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=5;HaplotypeScore=23.45;MQ=49.01;MQ0=1;QD=0.27;SB=83.26	GT:AD:DP:GL:GQ	0/1:55,18:51:-20.62,-15.37,-156.17:52.53
+20	10026357	rs685723	T	C	589.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1010.93;QD=16.57;SB=-474.08	GT:AD:DP:GL:GQ	0/1:26,35:60:-122.45,-18.07,-104.85:99
+20	10026794	rs687514	C	T	152.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1015.27;QD=19.52;SB=-447.00	GT:AD:DP:GL:GQ	0/1:19,32:49:-119.58,-14.77,-61.54:99
+20	10027868	rs514832	A	G	410.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.47;MQ0=0;OQ=1149.09;QD=13.21;SB=-556.55	GT:AD:DP:GL:GQ	0/1:43,44:87:-144.42,-26.22,-173.75:99
+20	10027872	rs594811	A	G	112.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.44;MQ0=0;OQ=1351.31;QD=16.28;SB=-565.56	GT:AD:DP:GL:GQ	0/1:39,44:83:-163.41,-25.00,-161.96:99
+20	10030188	rs652633	T	A	473.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.71;MQ0=0;OQ=1186.53;QD=15.02;SB=-453.42	GT:AD:DP:GL:GQ	0/1:41,38:79:-145.73,-23.79,-157.38:99
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+20	10031798	rs669985	G	A	353.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=4247.21;QD=40.84;SB=-1915.55	GT:AD:DP:GL:GQ	1/1:0,104:104:-423.72,-31.33,-0.03:99
+20	10031827	rs558493	C	T	27.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.83;MQ0=0;OQ=1957.26;QD=18.12;SB=-1004.58	GT:AD:DP:GL:GQ	0/1:52,56:108:-231.54,-32.53,-189.42:99
+20	10032094	rs681750	G	A	562.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.21;QD=14.16;SB=-575.44	GT:AD:DP:GL:GQ	0/1:47,36:82:-145.51,-24.71,-151.92:99
+20	10032413	rs683145	T	G	535.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=698.84;QD=11.09;SB=-317.98	GT:AD:DP:GL:GQ	0/1:33,30:63:-92.15,-18.98,-124.49:99
+20	10032882	rs479039	A	T	24.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=0;HaplotypeScore=7.14;MQ=58.99;MQ0=0;OQ=1029.41;QD=13.73;SB=-439.55	GT:AD:DP:GL:GQ	0/1:40,34:73:-128.21,-21.99,-155.80:99
+20	10034306	rs604452	T	C	170.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.46;MQ0=0;OQ=667.43;QD=8.67;SB=-359.16	GT:AD:DP:GL:GQ	0/1:47,29:73:-92.02,-22.00,-181.63:99
+20	10037037	rs2327261	C	T	271.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.97;MQ0=0;OQ=1384.69;QD=17.53;SB=-468.51	GT:AD:DP:GL:GQ	0/1:38,41:74:-164.05,-22.30,-111.89:99
+20	10037709	rs518364	A	T	403.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.68;MQ0=0;OQ=896.68;QD=12.63;SB=-381.55	GT:AD:DP:GL:GQ	0/1:39,32:70:-114.04,-21.09,-148.36:99
+20	10039371	rs678696	T	G	586.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1105.57;QD=15.79;SB=-406.66	GT:AD:DP:GL:GQ	0/1:32,38:70:-134.92,-21.08,-120.34:99
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+20	10043002	.	A	T	147.57	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1103.68;QD=13.14;SB=-535.28	GT:AD:DP:GL:GQ	0/1:48,36:84:-138.95,-25.30,-175.62:99
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+20	10045078	rs674630	G	T	86.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=58.99;MQ0=0;OQ=2874.89;QD=36.39;SB=-1368.13	GT:AD:DP:GL:GQ	1/1:0,79:78:-291.09,-23.49,-0.02:99
+20	10045642	rs572752	G	C	658.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3374.18;QD=42.18;SB=-1455.16	GT:AD:DP:GL:GQ	1/1:0,80:79:-336.42,-23.81,-0.03:99
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+20	10050828	rs660454	T	C	314.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.73;MQ0=0;OQ=1072.85;QD=12.62;SB=-513.86	GT:AD:DP:GL:GQ	0/1:48,37:84:-135.87,-25.30,-193.36:99
+20	10051448	rs565455	T	C	358.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.41;MQ0=0;OQ=1005.69;QD=14.16;SB=-400.33	GT:AD:DP:GL:GQ	0/1:36,35:69:-124.64,-20.79,-133.98:99
+20	10052688	.	C	A	247.91	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=928.77;QD=12.06;SB=-460.78	GT:AD:DP:GL:GQ	0/1:45,32:77:-119.35,-23.19,-165.26:99
+20	10058022	rs531797	T	C	82.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=6.22;MQ=58.46;MQ0=0;OQ=872.91;QD=12.47;SB=-339.92	GT:AD:DP:GL:GQ	0/1:38,32:67:-110.76,-20.18,-144.54:99
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+20	10067264	rs530271	G	A	217.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.68;MQ0=0;OQ=2865.42;QD=39.80;SB=-1324.28	GT:AD:DP:GL:GQ	1/1:0,72:72:-290.15,-21.69,-0.02:99
+20	10067722	rs604416	A	C	278.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1822.34;QD=35.05;SB=-862.09	GT:AD:DP:GL:GQ	1/1:0,52:52:-185.83,-15.66,-0.02:99
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+20	10070602	rs6039684	T	C	187.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.71;MQ0=0;OQ=2364.76;QD=32.84;SB=-1139.10	GT:AD:DP:GL:GQ	1/1:0,72:69:-240.09,-20.79,-0.03:99
+20	10070936	.	T	A	3050.87	Indel	AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=58.76;MQ0=0;QD=37.67;SB=-1399.42	GT:AD:DP:GL:GQ	1/1:0,81:80:-308.69,-24.09,-0.02:99
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+20	10071890	rs6039685	T	C	547.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1748.72;QD=30.68;SB=-861.55	GT:AD:DP:GL:GQ	1/1:0,57:56:-178.51,-16.89,-0.05:99
+20	10072505	rs6032786	A	G	465.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1789.94;QD=28.41;SB=-916.44	GT:AD:DP:GL:GQ	1/1:0,63:57:-182.63,-17.19,-0.05:99
+20	10074187	.	A	G	68.82	PASS	AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2702.25;QD=35.09;SB=-1331.57	GT:AD:DP:GL:GQ	1/1:0,77:77:-273.84,-23.20,-0.03:99
+20	10074240	rs614270	T	C	574.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2989.29;QD=34.76;SB=-1439.46	GT:AD:DP:GL:GQ	1/1:0,85:83:-302.53,-25.00,-0.02:99
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+20	10077752	.	T	C	195.33	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1175.95;QD=14.89;SB=-463.61	GT:AD:DP:GL:GQ	0/1:34,45:79:-144.69,-23.81,-137.94:99
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+20	10081800	rs474169	C	T	600.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.62;QD=16.25;SB=-544.01	GT:AD:DP:GL:GQ	0/1:34,33:67:-132.33,-20.18,-122.19:99
+20	10082892	rs644145	C	T	208.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1601.32;QD=38.13;SB=-762.50	GT:AD:DP:GL:GQ	1/1:0,42:41:-163.73,-12.35,-0.01:99
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+20	10087394	rs608188	T	G	410.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=1428.70;QD=17.21;SB=-695.70	GT:AD:DP:GL:GQ	0/1:35,48:83:-171.15,-25.00,-131.95:99
+20	10087754	rs544718	T	G	209.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=60.45;MQ0=0;OQ=1195.66;QD=15.33;SB=-504.83	GT:AD:DP:GL:GQ	0/1:36,42:77:-146.04,-23.19,-131.14:99
+20	10087804	rs609932	C	T	337.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=60.49;MQ0=0;OQ=1534.51;QD=15.35;SB=-666.41	GT:AD:DP:GL:GQ	0/1:50,50:93:-184.76,-28.03,-153.45:99
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+20	10088736	rs624401	A	C	166.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=51.41;MQ0=0;OQ=755.82;QD=12.81;SB=-289.77	GT:AD:DP:GL:GQ	0/1:29,29:53:-94.83,-15.97,-94.03:99
+20	10088747	rs624419	A	G	458.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=732.27;QD=13.31;SB=-319.26	GT:AD:DP:GL:GQ	0/1:25,30:54:-92.79,-16.28,-99.03:99
+20	10088799	rs624824	G	A	1.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.24;MQ0=0;OQ=1015.57;QD=18.46;SB=-384.14	GT:AD:DP:GL:GQ	0/1:24,31:54:-121.12,-16.28,-76.29:99
+20	10088895	rs500269	C	T	289	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.39;MQ0=0;OQ=522.39;QD=12.74;SB=-237.72	GT:AD:DP:GL:GQ	0/1:24,17:39:-67.28,-11.76,-70.34:99
+20	10088985	rs2876185	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=28.26;MQ=49.95;MQ0=0;OQ=805.93;QD=10.20;SB=-330.82	GT:AD:DP:GL:GQ	0/1:43,35:73:-105.88,-22.00,-156.93:99
+20	10089441	rs637625	A	G	358.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=992.46;QD=13.23;SB=-330.00	GT:AD:DP:GL:GQ	0/1:37,38:73:-124.53,-22.00,-148.03:99
+20	10089525	rs526819	C	T	411.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.84;MQ0=0;OQ=1526.59;QD=17.96;SB=-694.71	GT:AD:DP:GL:GQ	0/1:41,44:82:-180.66,-24.71,-123.55:99
+20	10090764	rs670562	A	G	90.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=59.44;MQ0=0;OQ=705.16;QD=10.52;SB=-326.14	GT:AD:DP:GL:GQ	0/1:37,30:65:-93.39,-19.59,-148.34:99
+20	10090970	rs671426	T	C	386.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.73;MQ0=0;OQ=1093.51;QD=15.62;SB=-550.11	GT:AD:DP:GL:GQ	0/1:33,37:67:-132.81,-20.18,-125.76:99
+20	10091214	rs563455	C	T	321.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.75;MQ0=0;OQ=1276.23;QD=17.02;SB=-480.51	GT:AD:DP:GL:GQ	0/1:36,39:73:-152.90,-21.99,-128.97:99
+20	10092415	rs590717	A	G	409.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1457.26;QD=14.57;SB=-743.58	GT:AD:DP:GL:GQ	0/1:51,49:100:-179.13,-30.12,-213.26:99
+20	10092927	.	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=8.09;MQ=59.09;MQ0=0;OQ=102.52;QD=1.35;SB=110.34	GT:AD:DP:GL:GQ	0/1:58,17:57:-30.71,-17.17,-163.94:99
+20	10093923	rs2423481	T	A	501.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=952.53;QD=14.65;SB=-490.92	GT:AD:DP:GL:GQ	0/1:33,32:64:-117.81,-19.28,-126.25:99
+20	10094251	rs543895	T	A	466.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.29;QD=18.66;SB=-397.80	GT:AD:DP:GL:GQ	0/1:26,37:59:-138.58,-17.77,-89.00:99
+20	10094582	rs56124148	A	G	315.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.72;MQ0=0;OQ=736.10;QD=11.15;SB=-314.87	GT:AD:DP:GL:GQ	0/1:38,28:65:-96.47,-19.58,-152.04:99
+20	10094774	rs570383	C	T	361.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=1017.49;QD=13.75;SB=-374.10	GT:AD:DP:GL:GQ	0/1:39,35:69:-125.82,-20.79,-130.93:99
+20	10095741	rs489548	A	G	80.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=57.01;MQ0=0;OQ=943.34;QD=13.29;SB=-405.22	GT:AD:DP:GL:GQ	0/1:36,34:68:-118.10,-20.48,-142.28:99
+20	10096293	rs515940	C	T	94.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.19;MQ0=0;OQ=1320.58;QD=17.61;SB=-665.71	GT:AD:DP:GL:GQ	0/1:37,38:74:-157.63,-22.29,-130.19:99
+20	10096596	rs518701	C	T	23.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.03;MQ0=0;OQ=1543.46;QD=17.95;SB=-788.95	GT:AD:DP:GL:GQ	0/1:40,46:85:-183.24,-25.61,-136.84:99
+20	10096768	rs520453	A	C	398.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1343.01;QD=15.44;SB=-695.73	GT:AD:DP:GL:GQ	0/1:42,45:87:-163.78,-26.20,-154.89:99
+20	10096899	rs652086	G	T	1162.66	Indel	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.76;MQ0=0;QD=14.72;SB=-335.13	GT:AD:DP:GL:GQ	0/1:39,40:78:-143.04,-23.49,-142.37:99
+20	10096933	rs652126	G	C	307.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1416.78;QD=16.87;SB=-379.18	GT:AD:DP:GL:GQ	0/1:45,39:83:-169.97,-25.01,-193.85:99
+20	10096958	rs652494	G	A	342.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.79;MQ0=0;OQ=1501.31;QD=16.68;SB=-462.96	GT:AD:DP:GL:GQ	0/1:45,45:87:-179.62,-26.20,-157.70:99
+20	10097075	rs6077657	T	G	299.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=1264.80;QD=13.75;SB=-586.94	GT:AD:DP:GL:GQ	0/1:44,48:90:-156.87,-27.11,-157.64:99
+20	10097437	rs11698147	T	C	519.38	Indel	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.01;HRun=1;HaplotypeScore=8.62;MQ=55.90;MQ0=0;QD=7.75;SB=-133.24	GT:AD:DP:GL:GQ	0/1:45,21:62:-73.60,-18.38,-162.59:99
+20	10097465	.	C	T	31.87	LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=3;HaplotypeScore=12.58;MQ=57.18;MQ0=0;QD=0.61;SB=-33.97	GT:AD:DP:GL:GQ	0/1:46,5:49:-20.93,-14.46,-150.67:64.70
+20	10097626	rs665397	C	A	205.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.09;MQ0=0;OQ=521.22;QD=11.33;SB=-241.94	GT:AD:DP:GL:GQ	0/1:27,19:45:-68.96,-13.55,-93.68:99
+20	10097789	rs550824	T	C	40.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.80;MQ=57.53;MQ0=1;OQ=609.05;QD=10.15;SB=-279.29	GT:AD:DP:GL:GQ	0/1:35,25:57:-81.36,-17.17,-136.53:99
+20	10097928	rs666732	G	A	147.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.09;MQ0=0;OQ=647.39;QD=16.60;SB=-318.83	GT:AD:DP:GL:GQ	0/1:17,22:38:-79.48,-11.45,-61.53:99
+20	10098110	rs6108402	G	C	43.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=639.58;QD=17.77;SB=-86.92	GT:AD:DP:GL:GQ	0/1:19,17:35:-77.79,-10.55,-73.75:99
+20	10098135	rs6108403	C	A	5.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.93;MQ0=0;OQ=389.51;QD=10.25;SB=-43.38	GT:AD:DP:GL:GQ	0/1:24,14:38:-53.68,-11.44,-83.52:99
+20	10098237	.	A	T	39.55	PASS	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.32;MQ0=0;OQ=159.94;QD=12.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,6:13:-23.19,-3.92,-25.88:99
+20	10098265	.	T	C	37.58	PASS	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.10;MQ0=0;OQ=64.00;QD=12.80;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,3:5:-11.19,-1.51,-7.23:57.28
+20	10098344	.	A	G	24.50	LowQual	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=6.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,2:4:-6.94,-1.20,-8.11:57.33
+20	10098786	.	C	T	16.33	LowQual	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=54.65;MQ0=0;QD=1.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,2:9:-7.62,-2.71,-21.38:49.06
+20	10098945	rs56176249	T	C	5.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=51.33;MQ0=0;OQ=363.84;QD=17.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,13:20:-45.69,-6.02,-27.59:99
+20	10098987	.	C	T	11	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.90;MQ0=0;OQ=342.06;QD=14.87;SB=-3.99	GT:AD:DP:GL:GQ	0/1:10,13:21:-43.82,-6.33,-33.84:99
+20	10099029	rs13044987	T	C	3.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.87;MQ0=0;OQ=125.69;QD=4.66;SB=2.03	GT:AD:DP:GL:GQ	0/1:18,9:25:-23.39,-7.53,-70.35:99
+20	10099034	rs13043768	C	A	139.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.19;MQ0=0;OQ=176.63;QD=6.31;SB=-31.94	GT:AD:DP:GL:GQ	0/1:18,10:26:-28.78,-7.84,-59.75:99
+20	10099044	rs13043626	A	C	29.61	LowQual	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=51.36;MQ0=0;QD=1.29;SB=-14.48	GT:AD:DP:GL:GQ	0/1:16,7:15:-10.76,-4.52,-43.68:62.44
+20	10099055	rs13045001	T	C	65.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=48.67;MQ0=0;OQ=222.63;QD=7.95;SB=-64.86	GT:AD:DP:GL:GQ	0/1:16,12:23:-32.47,-6.93,-57.23:99
+20	10099079	rs13043786	C	T	16.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=5.99;MQ=49.66;MQ0=0;OQ=370.70;QD=10.59;SB=-162.25	GT:AD:DP:GL:GQ	0/1:21,14:31:-49.70,-9.35,-56.03:99
+20	10099140	rs585009	G	T	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=2.65;MQ=55.73;MQ0=0;OQ=847.58;QD=14.13;SB=-233.91	GT:AD:DP:GL:GQ	0/1:30,30:58:-105.51,-17.47,-102.15:99
+20	10099190	rs508242	G	T	210.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.42;MQ0=0;OQ=860.99;QD=13.25;SB=-270.28	GT:AD:DP:GL:GQ	0/1:33,32:62:-108.05,-18.67,-118.91:99
+20	10099220	rs585404	A	G	5.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=6.00;MQ=56.96;MQ0=0;OQ=481.07;QD=10.46;SB=-187.61	GT:AD:DP:GL:GQ	0/1:25,21:43:-64.35,-12.96,-100.07:99
+20	10099250	rs585439	G	A	100.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=56.23;MQ0=0;OQ=672.67;QD=17.70;SB=-330.34	GT:AD:DP:GL:GQ	0/1:17,21:36:-81.41,-10.86,-48.14:99
+20	10099535	rs586791	G	A	209.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.28;MQ0=0;OQ=1326.40;QD=20.73;SB=-582.88	GT:AD:DP:GL:GQ	0/1:25,38:62:-157.48,-21.55,-76.17:99
+20	10099565	rs532882	C	T	44.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.99;MQ=59.66;MQ0=0;OQ=1282.88;QD=19.15;SB=-617.46	GT:AD:DP:GL:GQ	0/1:30,37:67:-151.75,-20.18,-103.68:99
+20	10099755	rs534687	C	T	66.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=1091.00;QD=16.78;SB=-547.75	GT:AD:DP:GL:GQ	0/1:32,33:64:-131.66,-19.27,-116.96:99
+20	10099832	rs534882	A	G	477.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=927.85;QD=12.89;SB=-445.10	GT:AD:DP:GL:GQ	0/1:39,33:71:-117.45,-21.39,-156.97:99

public/testdata/PhaseByTransmission.IntegrationTest.FP.vcf

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##PhaseByTransmissionUnitTest="This file contains only genotypes with false mendelian violations in the input data. The output data should correct the genotypes and phase the trios. The pair should be corrected and phased where possible. Genotype combination phred score should be reported where possible. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
+1	10109	.	A	T	99	PASS	TestDescription=HomRef/HomRef/Het	GT:GQ:PL	0/0:50:0,50,200	0/0:40:0,40,200	0/1:30:30,0,200	0/0:50:0,50,200	0/1:30:30,0,200	0/0:50:0,50,200	
+1	10147	.	C	A	99	PASS	TestDescription=HomRef/HomRef/HomAlt	GT:GQ:PL	0/0:30:0,30,200	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
+1	10150	.	C	T	99	PASS	TestDescription=HomRef/Het/HomAlt	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	1/1:50:200,50,0	0/0:40:0,40,200	1/1:50:200,50,0	0/0:40:0,40,200
+1	10177	.	A	C	99	PASS	TestDescription=HomRef/HomAlt/HomRef	GT:GQ:PL	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	0/0:50:0,50,200	0/0:30:0,30,200	0/0:50:0,50,200
+1	10180	.	T	C	99	PASS	TestDescription=HomRef/HomAlt/HomAlt	GT:GQ:PL	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
+1	10234	.	C	T	99	PASS	TestDescription=Het/HomRef/HomAlt	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/1:40:40,0,200	1/1:50:200,50,0	0/1:40:40,0,200
+1	10235	.	T	A	99	PASS	TestDescription=Het/HomAlt/HomRef	GT:GQ:PL	0/1:50:50,0,200	1/1:40:200,40,0	0/0:30:0,30,200	0/1:50:50,0,200	0/0:30:0,30,200	0/1:50:50,0,200
+1	10236	.	A	G	99	PASS	TestDescription=HomVar/HomRef/HomRef	GT:GQ:PL	1/1:30:200,30,0	0/0:50:0,50,200	0/0:40:0,40,200	1/1:30:200,30,0	0/0:50:0,50,200	1/1:30:200,30,0
+1	10250	.	A	C	99	PASS	TestDescription=HomVar/HomRef/HomVar	GT:GQ:PL	1/1:40:200,40,0	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	1/1:50:200,50,0	1/1:40:200,40,0
+1	10257	.	A	C	99	PASS	TestDescription=HomVar/Het/HomRef	GT:GQ:PL	1/1:50:200,50,0	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/0:30:0,30,200	1/1:50:200,50,0
+1	10285	.	T	C	99	PASS	TestDescription=HomVar/HomVar/Het	GT:GQ:PL	1/1:30:200,30,0	1/1:50:200,50,0	0/1:40:40,0,200	1/1:30:200,30,0	0/1:40:40,0,200	1/1:30:200,30,0
+1	10297	.	C	T	99	PASS	TestDescription=HomVar/HomVar/HomRef	GT:GQ:PL	1/1:40:200,40,0	1/1:30:200,30,0	0/0:50:0,50,200	1/1:40:200,40,0	0/0:50:0,50,200	1/1:40:200,40,0

public/testdata/PhaseByTransmission.IntegrationTest.Special.vcf

@@ -0,0 +1,20 @@
+##fileformat=VCFv4.0
+##PhaseByTransmissionUnitTest="This file contains special cases for phasing by transmission such as missing genotypes. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
+1	10109	.	A	T	99	PASS	TestDescription=NoCall_mother	GT:GQ:PL	./.:.:.	0/0:40:0,40,200	0/1:30:30,0,200	./.:.:.	0/1:30:30,0,200	./.:.:.	
+1	10147	.	C	A	99	PASS	TestDescription=NoCall_father	GT:GQ:PL	0/0:30:0,30,200	./.:.:.	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
+1	10150	.	C	T	99	PASS	TestDescription=NoCall_child	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	./.:.:.	0/0:40:0,40,200	./.:.:.	0/0:40:0,40,200
+1	10177	.	A	C	99	PASS	TestDescription=Missing_mother	GT:GQ:PL	.	1/1:40:200,40,0	0/0:30:0,30,200	.	0/0:30:0,30,200	.
+1	10180	.	T	C	99	PASS	TestDescription=Missing_father	GT:GQ:PL	0/0:30:0,30,200	.	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
+1	10234	.	C	T	99	PASS	TestDescription=Missing_child	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	.	0/1:40:40,0,200	.	0/1:40:40,0,200
+1	10235	.	T	A	99	PASS	TestDescription=NoCall_parents	GT:GQ:PL	./.:.:.	./.:.:.	0/0:30:0,30,200	./.:.:.	0/0:30:0,30,200	./.:.:.
+1	10236	.	A	G	99	PASS	TestDescription=NoCall_all	GT:GQ:PL	./.:.:.	./.:.:.	./.:.:.	./.:.:.	./.:.:.	./.:.:.
+1	10250	.	A	C	99	PASS	TestDescription=Missing_parents	GT:GQ:PL	.	.	1/1:50:200,50,0	.	1/1:50:200,50,0	.
+1	10257	.	A	C	99	PASS	TestDescription=Missing_all	GT:GQ:PL	.	.	.	.	.	.
+1	10285	.	T	C	99	PASS	TestDescription=ZeroConfidence	GT:GQ:PL	0/1:0:0,0,0	1/1:0:0,0,0	1/1:0:0,0,0	0/1:0:0,0,0	1/1:0:0,0,0	0/1:0:0,0,0
+1	10297	.	C	T	99	PASS	TestDescription=ZeroConfidenceParents	GT:GQ:PL	1/1:0:0,0,0	0/0:0:0,0,0	0/1:10:10,0,50	1/1:0:0,0,0	0/1:10:10,0,50	1/1:0:0,0,0
+1	10304	.	A	C	99	PASS	TestDescription=ZeroConfidenceChild	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:0:0,0,0	1/1:50:200,50,0	0/1:0:0,0,0	1/1:50:200,50,0

public/testdata/PhaseByTransmission.IntegrationTest.TN.vcf

@@ -0,0 +1,22 @@
+##fileformat=VCFv4.0
+##PhaseByTransmissionUnitTest="This file contains only genotypes of high quality and no mendelian violation in the input data. The output data should phase the trio and pair except for the Het/Het/Het case and leave the unrelated individual untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
+1	10109	.	A	T	99	PASS	TestDescription=HomRef/HomRef/HomRef	GT:GQ:PL	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	
+1	10147	.	C	A	99	PASS	TestDescription=HomRef/Het/HomRef	GT:GQ:PL	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	
+1	10150	.	C	T	99	PASS	TestDescription=HomRef/Het/Het	GT:GQ:PL	0/0:50:0,50,200	0/1:50:50,0,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200
+1	10177	.	A	C	99	PASS	TestDescription=HomRef/HomAlt/Het	GT:GQ:PL	0/0:50:0,50,200	1/1:50:200,50,0	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200
+1	10180	.	T	C	99	PASS	TestDescription=Het/HomRef/HomRef	GT:GQ:PL	0/1:50:50,0,200	0/0:50:0,50,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200
+1	10234	.	C	T	99	PASS	TestDescription=Het/HomRef/Het	GT:GQ:PL	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200
+1	10235	.	T	A	99	PASS	TestDescription=Het/Het/HomRef	GT:GQ:PL	0/1:50:50,0,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200
+1	10236	.	A	G	99	PASS	TestDescription=Het/Het/Het	GT:GQ:PL	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200
+1	10250	.	A	C	99	PASS	TestDescription=Het/Het/HomVar	GT:GQ:PL	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:50,0,200
+1	10257	.	A	C	99	PASS	TestDescription=Het/HomVar/Het	GT:GQ:PL	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	0/1:50:50,0,200	0/1:50:200,0,50	0/1:50:50,0,200
+1	10285	.	T	C	99	PASS	TestDescription=Het/HomVar/HomVar	GT:GQ:PL	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:50,0,200
+1	10297	.	C	T	99	PASS	TestDescription=HomVar/HomRef/Het	GT:GQ:PL	1/1:50:200,50,0	0/0:50:0,50,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
+1	10304	.	A	C	99	PASS	TestDescription=HomVar/Het/Het	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
+1	10310	.	A	C	99	PASS	TestDescription=HomVar/Het/HomVar	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0
+1	10315	.	C	T	99	PASS	TestDescription=HomVar/HomVar/HomVar	GT:GQ:PL	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0

public/testdata/PhaseByTransmission.IntegrationTest.TP.vcf

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##PhaseByTransmissionUnitTest="This file contains only genotypes of high quality true mendelian violations in the input data. The output data should not be able to phase the trios. The pair is phased where there is not enough information to distinguish a MV from a correct descent. Genotype combination phred score should be reported where possible. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
+1	10109	.	A	T	99	PASS	TestDescription=HomRef/HomRef/Het	GT:GQ:PL	0/0:80:0,80,200	0/0:80:0,80,200	0/1:80:80,0,200	0/0:80:0,80,200	0/1:80:80,0,200	0/0:80:0,80,200	
+1	10147	.	C	A	99	PASS	TestDescription=HomRef/HomRef/HomAlt	GT:GQ:PL	0/0:80:0,80,200	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	
+1	10150	.	C	T	99	PASS	TestDescription=HomRef/Het/HomAlt	GT:GQ:PL	0/0:80:0,80,200	0/1:80:80,0,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200
+1	10177	.	A	C	99	PASS	TestDescription=HomRef/HomAlt/HomRef	GT:GQ:PL	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	0/0:80:0,80,200	0/0:80:0,80,200	0/0:80:0,80,200
+1	10180	.	T	C	99	PASS	TestDescription=HomRef/HomAlt/HomAlt	GT:GQ:PL	0/0:80:0,80,200	1/1:80:200,80,0	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200
+1	10234	.	C	T	99	PASS	TestDescription=Het/HomRef/HomAlt	GT:GQ:PL	0/1:80:80,0,200	0/0:80:0,80,200	1/1:80:200,80,0	0/1:80:80,0,200	1/1:80:200,80,0	0/1:80:80,0,200
+1	10235	.	T	A	99	PASS	TestDescription=Het/HomAlt/HomRef	GT:GQ:PL	0/1:80:80,0,200	1/1:80:200,80,0	0/0:80:0,80,200	0/1:80:80,0,200	0/0:80:0,80,200	0/1:80:80,0,200
+1	10236	.	A	G	99	PASS	TestDescription=HomVar/HomRef/HomRef	GT:GQ:PL	1/1:80:200,80,0	0/0:80:0,80,200	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0
+1	10250	.	A	C	99	PASS	TestDescription=HomVar/HomRef/HomVar	GT:GQ:PL	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	1/1:80:200,80,0	1/1:80:200,80,0	1/1:80:200,80,0
+1	10257	.	A	C	99	PASS	TestDescription=HomVar/Het/HomRef	GT:GQ:PL	1/1:80:200,80,0	0/1:80:80,0,200	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0
+1	10285	.	T	C	99	PASS	TestDescription=HomVar/HomVar/Het	GT:GQ:PL	1/1:80:200,80,0	1/1:80:200,80,0	0/1:80:80,0,200	1/1:80:200,80,0	0/1:80:80,0,200	1/1:80:200,80,0
+1	10297	.	C	T	99	PASS	TestDescription=HomVar/HomVar/HomRef	GT:GQ:PL	1/1:80:200,80,0	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0

public/testdata/PhaseByTransmission.IntegrationTest.goodFamilies.ped

@@ -0,0 +1,6 @@
+TRIO	TRIO_MOTHER	0	0	0	-9
+TRIO	TRIO_FATHER	0	0	1	-9
+TRIO	TRIO_CHILD	TRIO_FATHER	TRIO_MOTHER	0	-9
+PAIR	PAIR_FATHER	0	0	0	-9
+PAIR	PAIR_CHILD	PAIR_FATHER	0	1	-9
+UNRELATED	UNRELATED_INDIVIDUAL_CONTROL	0	0	0	-9

public/testdata/ROD_validation/always_reindex.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.0
+##fileDate=20090908
+##source=QCALLv1.0
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
+1	17786644	rs34417109	G	A	60.0	PASS	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	

public/testdata/ROD_validation/newerTribbleTrack.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.0
+##fileDate=20090908
+##source=QCALLv1.0
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
+1	17786644	rs34417109	G	A	60.0	PASS	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	

public/testdata/ROD_validation/read_only/good_index.vcf

@@ -0,0 +1,7 @@
+##format=VCRv3.2
+##fileDate=20090908
+##source=QCALLv1.0
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
+1	17786644	rs34417109	G	A	60.0	0	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	

public/testdata/ROD_validation/read_only/no_index.vcf

@@ -0,0 +1,7 @@
+##format=VCRv3.2
+##fileDate=20090908
+##source=QCALLv1.0
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
+1	17786644	rs34417109	G	A	60.0	0	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	

public/testdata/ROD_validation/read_only/relic.vcf

@@ -0,0 +1,7 @@
+##format=VCRv3.2
+##fileDate=20090908
+##source=QCALLv1.0
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
+1	17786644	rs34417109	G	A	60.0	0	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	

public/testdata/VQSR.mixedTest.input

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	1000177	.	C	T	345	PASS	AC=43;AF=0.02053;AN=2094;BaseQRankSum=-0.234;DP=3748;DS;FS=5.678;HRun=2;HaplotypeScore=35.9850;InbreedingCoeff=0.0715;MQ=67.54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;set=EUR.admix
+20	1000177	.	CA	C	82.64	PASS	AC=43;AF=0.02053;AN=2094;BaseQRankSum=-0.234;DP=3748;DS;FS=5.678;HRun=2;HaplotypeScore=35.9850;InbreedingCoeff=0.0715;MQ=67.54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;set=EUR.admix
+20	1000382	.	C	G	456	PASS	AC=19;AF=0.00996;AN=1908;BaseQRankSum=3.153;DP=1249;FS=12.307;HRun=0;HaplotypeScore=25.9702;InbreedingCoeff=0.0716;MQ=49.54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;set=ASN.admix
+20	1000382	.	CCAAT	C	246.44	PASS	AC=19;AF=0.00996;AN=1908;BaseQRankSum=3.153;DP=1249;FS=12.307;HRun=0;HaplotypeScore=25.9702;InbreedingCoeff=0.0716;MQ=49.54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;set=ASN.admix
+20	1000442	rs112800484	TTTCA	T	28592.75	PASS	AC=1034;AF=0.69583;AN=1486;BaseQRankSum=19.864;DB;DP=1304;FS=31.497;HRun=0;HaplotypeScore=17.6398;InbreedingCoeff=0.2728;MQ=46.55;MQ0=85;MQRankSum=-6.417;QD=30.65;ReadPosRankSum=-2.058;set=EUR.admix

public/testdata/VQSR.mixedTest.recal

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	
+20	1000177	.	N	<VQSR>	.	.	END=1000177;VQSLOD=-1.2345;culprit=FS
+20	1000177	.	N	<VQSR>	.	.	END=1000178;VQSLOD=-1.2377;culprit=HaplotypeScore
+20	1000382	.	N	<VQSR>	.	.	END=1000386;VQSLOD=-0.5534;culprit=HaplotypeScore
+20	1000382	.	N	<VQSR>	.	.	END=1000382;VQSLOD=-0.5678;culprit=FS
+20	1000442	.	N	<VQSR>	.	.	END=1000446;VQSLOD=3.5923;culprit=QD

public/testdata/VQSR.mixedTest.tranches

@@ -0,0 +1,7 @@
+# Variant quality score tranches file
+# Version number 4
+targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,accessibleTruthSites,callsAtTruthSites,truthSensitivity
+90.00,17160,9743,0.0000,0.0000,2.3848,TruthSensitivityTranche0.00to90.00,9065,8158,0.8999
+99.00,21283,82814,0.0000,0.0000,-1.2413,TruthSensitivityTranche90.00to99.00,9065,8974,0.9900
+99.90,21845,92768,0.0000,0.0000,-6.9203,TruthSensitivityTranche99.00to99.90,9065,9055,0.9989
+100.00,21969,94464,0.0000,0.0000,-402.3663,TruthSensitivityTranche99.90to100.00,9065,9065,1.0000

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.HG00625.vcf

@@ -0,0 +1,25 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Validation_Data/VariantEval/FundamentalsTest.annotated.db.subset.final.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=[HG00625] select_expressions=[] excludeNonVariants=false excludeFiltered=false"
+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=1	GT:DP:GQ:PL	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=3	GT:DP:GQ:PL	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.
+20	10019093	rs575534	A	G	69795.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	1/1:5:15:172,15,0
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=2;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DP=1;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:4:12:139,12,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.NA12045.vcf

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12045
+20	10003358	rs926982	A	C	92318.04	PASS	DBSNP129;DBSNP132;DP=5	GT:DP:GQ:PL	0/1:5:51:51,0,95
+20	10003692	rs2064653	A	G	119873.04	PASS	DBSNP129;DBSNP132;DP=4	GT:DP:GQ:PL	0/1:4:20:20,0,85
+20	10015679	rs113024248	C	.	2829.33	PASS	DBSNP132;DP=0;OMNI	GT:DP:PL	./.
+20	10015790	rs114356776	G	.	43.60	PASS	DBSNP132;DP=0	GT:DP:PL	./.
+20	10019093	rs575534	A	G	69795.04	PASS	DBSNP129;DBSNP132;DP=6;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
+20	10019169	rs7260784	C	.	1193.61	PASS	DBSNP129;DBSNP132;DP=6;HAPMAP;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
+20	10032432	rs78089752	A	.	367.04	PASS	DBSNP132;DP=8;OMNI	GT:DP:GQ:PL	0/0:8:24:0,24,293
+20	10037119	.	G	.	469.85	PASS	DBSNP129;DP=2	GT:DP:GQ:PL	0/0:2:6:0,6,65
+20	10047435	rs598275	G	A	82495.04	PASS	DBSNP129;DBSNP132;DP=2;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
+20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf

@@ -0,0 +1,18 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.vcf

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
+20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.snps_and_indels.vcf

@@ -0,0 +1,26 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	PASS	NONCPG;AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338
+20	10003358	rs926982	A	C	92318.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
+20	10003692	rs2064653	A	G	119873.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+20	10015679	rs113024248	C	.	2829.33	PASS	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	FAIL	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
+20	10019093	rs575534	A	G	69795.04	PASS	NONCPG;AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
+20	10019169	rs7260784	C	.	1193.61	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
+20	10032432	rs78089752	A	.	367.04	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
+20	10037119	.	G	.	469.85	PASS	NONCPG;AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
+20	10047435	rs598275	G	A	82495.04	FAIL	CPG;AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0
+20	31384616	.	A	AG	12610.94	PASS	NONCPG;AC=96;AF=0.5000;AN=192;DP=5288;Dels=0.00;HRun=2;HaplotypeScore=9.2447;MQ=61.14;MQ0=0;QD=2.38;SB=-2.03;sumGLbyD=2.39	GT:DP:GQ:PL	0/1:50:99:161,0,486	0/1:55:99:123,0,615	0/1:51:87.95:88,0,647
+20	62172300	.	CGG	C	440.96	FAIL	CPG;AC=25;AF=0.1316;AN=190;DP=2673;Dels=0.01;HRun=1;HaplotypeScore=12.2310;MQ=58.24;MQ0=0;QD=0.63;SB=-58.90;sumGLbyD=1.00	GT:DP:GQ:PL	0/0:29:45.69:0,46,1437	0/0:16:16.13:0,16,799	0/1:31:32.81:33,0,1141

public/testdata/VariantEval/MendelianViolationEval.ped

@@ -0,0 +1,6 @@
+TRIO	TRIO_MOTHER	0	0	0	-9
+TRIO	TRIO_FATHER	0	0	1	-9
+TRIO	TRIO_CHILD	TRIO_MOTHER	TRIO_FATHER	0	-9
+PAIR	PAIR_PARENT	0	0	0	-9
+PAIR	PAIR_CHILD	PAIR_PARENT	0	1	-9
+UNRELATED	UNRELATED_INDIVIDUAL_CONTROL	0	0	0	-9

public/testdata/VariantEval/MendelianViolationEval.vcf

@@ -0,0 +1,22 @@
+##fileformat=VCFv4.0
+##MendelianViolationEvaluator="This file contains genotypes with mendelian violations in the input data. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_PARENT	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
+1	10109	.	A	T	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	0/0:40:0,40,200	0/1:30:30,0,200	0/0:50:0,50,200	0/1:30:30,0,200	0/0:50:0,50,200	
+1	10147	.	C	A	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
+1	10150	.	C	T	99	PASS	.	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	1/1:50:200,50,0	0/0:40:0,40,200	1/1:50:200,50,0	0/0:40:0,40,200
+1	10177	.	A	C	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	0/0:50:0,50,200	0/0:30:0,30,200	0/0:50:0,50,200
+1	10180	.	T	C	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
+1	10234	.	C	T	99	PASS	.	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/1:40:40,0,200	1/1:50:200,50,0	0/1:40:40,0,200
+1	10235	.	T	A	99	PASS	.	GT:GQ:PL	0/1:50:50,0,200	1/1:40:200,40,0	0/0:30:0,30,200	0/1:50:50,0,200	0/0:30:0,30,200	0/1:50:50,0,200
+1	10236	.	A	G	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	0/0:50:0,50,200	0/0:40:0,40,200	1/1:30:200,30,0	0/0:50:0,50,200	1/1:30:200,30,0
+1	10250	.	A	C	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	1/1:50:200,50,0	1/1:40:200,40,0
+1	10257	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/0:30:0,30,200	1/1:50:200,50,0
+1	10285	.	T	C	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	1/1:50:200,50,0	0/1:40:40,0,200	1/1:30:200,30,0	0/1:40:40,0,200	1/1:30:200,30,0
+1	10297	.	C	T	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	1/1:30:200,30,0	0/0:50:0,50,200	1/1:40:200,40,0	0/0:50:0,50,200	1/1:40:200,40,0
+1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:0:0,0,0	1/1:50:200,50,0	0/1:0:0,0,0	1/1:50:200,50,0
+1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
+1	10310	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0
+1	10315	.	C	T	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0

public/testdata/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf

@@ -0,0 +1,243 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=ABFilter,Description="AB  0.75 && DP  40">
+##FILTER=<ID=DPFilter,Description="DP  120 || SB  -0.10">
+##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
+##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
+##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
+##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual  0.06">
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP))  0.1)">
+##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FilterLiftedVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/tmp/0.069557317373441.sorted.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=FilterLiftedVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##LiftoverVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/home/radon01/kiran/scr1/projects/DataProcessingPaper/results/newForStacey/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=LiftoverVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub chain=/humgen/gsa-hpprojects/GATK/data/Liftover_Chain_Files/hg18ToHg19.broad.over.chain newSequenceDictionary=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dict"
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:10000000-10100000] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false"
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,chrX] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
+##source=SelectVariants
+##source=VariantOptimizer
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	10000117	rs4816203	C	T	77.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=867.45;QD=13.77;SB=-268.09	GT:AD:DP:GL:GQ	0/1:36,27:63:-109.01,-18.98,-129.63:99
+20	10000211	rs4813908	C	T	273.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.66;MQ0=0;OQ=913.43;QD=16.61;SB=-383.86	GT:AD:DP:GL:GQ	0/1:28,27:53:-110.59,-15.96,-95.89:99
+20	10000439	rs4816204	T	G	489.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2354.98;QD=29.44;SB=-1083.04	GT:AD:DP:GL:GQ	1/1:0,80:77:-239.15,-23.21,-0.06:99
+20	10000598	rs6057087	T	A	659.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=1772.11;QD=36.92;SB=-761.69	GT:AD:DP:GL:GQ	1/1:0,48:48:-180.81,-14.46,-0.01:99
+20	10000694	rs6057088	G	A	276.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=49.18;MQ0=0;OQ=1128.96;QD=14.11;SB=-510.63	GT:AD:DP:GL:GQ	0/1:46,34:80:-140.27,-24.09,-169.48:99
+20	10000758	rs6057089	T	A	243.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.23;MQ0=0;OQ=3541.99;QD=38.92;SB=-1671.36	GT:AD:DP:GL:GQ	1/1:0,91:91:-353.20,-27.40,-0.02:99
+20	10001019	rs6077626	T	G	401.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.70;MQ0=2;OQ=712.45;QD=10.33;SB=-352.52	GT:AD:DP:GL:GQ	0/1:40,29:65:-94.10,-19.57,-146.27:99
+20	10001298	rs1535165	T	A	637.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.34;MQ0=0;OQ=2708.88;QD=36.61;SB=-1143.40	GT:AD:DP:GL:GQ	1/1:0,73:73:-274.49,-21.99,-0.02:99
+20	10001474	rs1535166	C	T	608.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.97;MQ0=0;OQ=2678.14;QD=38.26;SB=-1011.68	GT:AD:DP:GL:GQ	1/1:0,70:69:-271.42,-20.79,-0.02:99
+20	10001617	rs2876191	C	A	279.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.17;MQ0=0;OQ=1439.09;QD=14.25;SB=-481.71	GT:AD:DP:GL:GQ	0/1:52,49:101:-177.61,-30.42,-186.45:99
+20	10001628	rs1535167	G	A	101.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.36;MQ0=0;OQ=3780.26;QD=40.22;SB=-1550.04	GT:AD:DP:GL:GQ	1/1:0,93:93:-377.03,-30.13,-2.37:99
+20	10001661	rs1535168	T	C	621.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=2787.58;QD=34.41;SB=-1177.74	GT:AD:DP:GL:GQ	1/1:0,81:79:-282.37,-23.79,-0.02:99
+20	10001670	rs1535169	T	G	512.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.21;MQ0=0;OQ=2852.67;QD=35.22;SB=-1272.32	GT:AD:DP:GL:GQ	1/1:0,81:80:-288.87,-24.09,-0.02:99
+20	10002058	rs4404352	T	G	305.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.60;MQ0=0;OQ=2628.53;QD=34.14;SB=-934.22	GT:AD:DP:GL:GQ	1/1:1,76:75:-266.46,-22.59,-0.03:99
+20	10002099	rs4555427	C	T	2.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=5;HaplotypeScore=0.47;MQ=56.02;MQ0=0;OQ=1117.99;QD=17.47;SB=-498.13	GT:AD:DP:GL:GQ	0/1:27,37:61:-133.46,-18.38,-95.58:99
+20	10002138	rs4569544	C	G	481.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.30;MQ0=0;OQ=2204.77;QD=40.09;SB=-1043.64	GT:AD:DP:GL:GQ	1/1:0,55:51:-224.08,-15.37,-0.01:99
+20	10002142	rs4417777	G	C	579.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=2117.84;QD=39.22;SB=-975.74	GT:AD:DP:GL:GQ	1/1:0,54:49:-215.38,-14.76,-0.01:99
+20	10002470	rs2327260	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=11;HaplotypeScore=1.75;MQ=47.38;MQ0=0;OQ=2328.93;QD=34.25;SB=-1076.99	GT:AD:DP:GL:GQ	1/1:0,68:61:-236.50,-18.38,-0.02:99
+20	10002478	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=7;HaplotypeScore=9.60;MQ=53.59;MQ0=0;OQ=111.85;QD=2.00;SB=59.21	GT:AD:DP:GL:GQ	0/1:47,9:46:-28.33,-13.86,-140.18:99
+20	10002625	rs2144570	G	T	624.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=2238.72;QD=36.11;SB=-983.67	GT:AD:DP:GL:GQ	1/1:0,62:61:-227.47,-18.37,-0.01:99
+20	10003021	rs6057090	C	T	599.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2357.20;QD=38.64;SB=-1005.68	GT:AD:DP:GL:GQ	1/1:0,61:60:-239.32,-18.08,-0.02:99
+20	10003358	rs926982	A	C	283.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1239.40;QD=14.58;SB=-411.81	GT:AD:DP:GL:GQ	0/1:43,42:84:-152.52,-25.30,-151.13:99
+20	10003651	rs926984	T	C	632.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=3208.86;QD=35.65;SB=-1068.08	GT:AD:DP:GL:GQ	1/1:0,90:89:-324.50,-26.81,-0.03:99
+20	10003692	rs2064653	A	G	614.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=2247.29;QD=34.05;SB=-940.96	GT:AD:DP:GL:GQ	1/1:0,66:65:-228.34,-19.58,-0.03:99
+20	10003832	rs6057091	G	A	453.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=2581.24;QD=40.33;SB=-971.37	GT:AD:DP:GL:GQ	1/1:0,64:64:-261.72,-19.28,-0.01:99
+20	10004094	rs1988590	A	C	5.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=53.93;MQ0=0;OQ=1571.64;QD=30.82;SB=-600.05	GT:AD:DP:GL:GQ	1/1:0,51:46:-160.77,-13.86,-0.02:99
+20	10004147	rs1988591	A	G	22.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.77;MQ=56.98;MQ0=0;OQ=1621.26;QD=30.59;SB=-586.00	GT:AD:DP:GL:GQ	1/1:0,53:50:-165.75,-15.08,-0.04:99
+20	10004193	.	G	T	112	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.87;MQ0=0;OQ=817.22;QD=15.13;SB=-391.14	GT:AD:DP:GL:GQ	0/1:25,29:51:-100.37,-15.36,-82.85:99
+20	10004351	rs6057092	C	G	541.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2906.33;QD=42.74;SB=-1364.94	GT:AD:DP:GL:GQ	1/1:0,68:67:-294.24,-20.19,-0.02:99
+20	10004389	rs6057093	T	G	609.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.09;MQ0=0;OQ=2210.27;QD=35.65;SB=-884.11	GT:AD:DP:GL:GQ	1/1:0,62:62:-224.63,-18.68,-0.02:99
+20	10004610	rs2064654	A	C	2.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=10.08;MQ=58.45;MQ0=0;OQ=3199.99;QD=35.56;SB=-1545.20	GT:AD:DP:GL:GQ	1/1:1,89:88:-323.60,-26.50,-0.02:99
+20	10004725	rs10485737	A	G	457.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.27;MQ0=0;OQ=850.43;QD=13.08;SB=-367.17	GT:AD:DP:GL:GQ	0/1:35,30:65:-107.90,-19.58,-141.57:99
+20	10004874	rs725567	A	C	315.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.30;MQ0=0;OQ=2956.73;QD=35.20;SB=-1190.16	GT:AD:DP:GL:GQ	1/1:0,84:83:-299.28,-25.00,-0.02:99
+20	10004887	rs725566	A	G	256.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.44;MQ0=0;OQ=1129.32;QD=13.61;SB=-455.56	GT:AD:DP:GL:GQ	0/1:44,39:82:-140.92,-24.70,-171.36:99
+20	10005010	rs725565	C	T	706.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2824.42;QD=39.23;SB=-1089.38	GT:AD:DP:GL:GQ	1/1:0,72:71:-286.04,-21.39,-0.02:99
+20	10005427	rs6057094	C	T	587.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2155.03;QD=39.91;SB=-1081.37	GT:AD:DP:GL:GQ	1/1:0,54:54:-219.10,-16.26,-0.01:99
+20	10005499	rs6077631	A	G	634.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2607.55;QD=35.72;SB=-1078.12	GT:AD:DP:GL:GQ	1/1:0,73:73:-264.36,-21.99,-0.02:99
+20	10005587	rs6108375	A	G	498.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1061.48;QD=14.95;SB=-522.04	GT:AD:DP:GL:GQ	0/1:35,36:70:-130.52,-21.08,-138.09:99
+20	10005723	rs6108376	A	G	529.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2687.35;QD=31.62;SB=-1283.54	GT:AD:DP:GL:GQ	1/1:0,85:83:-272.38,-25.03,-0.06:99
+20	10006291	rs6118856	G	A	172.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=908.18;QD=11.08;SB=-459.38	GT:AD:DP:GL:GQ	0/1:53,29:82:-118.80,-24.70,-191.13:99
+20	10006404	rs926985	A	C	490.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2586.62;QD=33.59;SB=-921.26	GT:AD:DP:GL:GQ	1/1:0,77:75:-262.28,-22.59,-0.03:99
+20	10006682	rs6057095	T	A	131.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.43;MQ0=0;OQ=2662.92;QD=36.48;SB=-986.49	GT:AD:DP:GL:GQ	1/1:0,72:71:-269.90,-21.39,-0.02:99
+20	10007150	rs11904989	G	C	276.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.70;MQ0=0;OQ=742.20;QD=11.78;SB=-296.80	GT:AD:DP:GL:GQ	0/1:38,25:60:-95.59,-18.09,-157.44:99
+20	10007175	rs2207850	C	T	90.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.69;MQ0=0;OQ=1294.38;QD=21.22;SB=-604.18	GT:AD:DP:GL:GQ	0/1:22,39:58:-150.19,-17.47,-75.88:99
+20	10007352	rs1884399	C	T	614.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2708.19;QD=39.25;SB=-1162.02	GT:AD:DP:GL:GQ	1/1:0,69:68:-274.43,-20.49,-0.02:99
+20	10007531	rs1884400	A	G	493.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2611.60;QD=36.78;SB=-843.33	GT:AD:DP:GL:GQ	1/1:0,71:71:-264.76,-21.38,-0.02:99
+20	10007980	rs2876192	A	C	668.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.73;MQ0=0;OQ=3022.49;QD=34.35;SB=-1434.18	GT:AD:DP:GL:GQ	1/1:0,88:87:-305.86,-26.20,-0.03:99
+20	10008221	rs2876193	T	C	510.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.18;MQ0=0;OQ=2840.34;QD=36.41;SB=-1397.57	GT:AD:DP:GL:GQ	1/1:0,78:78:-287.64,-23.49,-0.02:99
+20	10008458	rs6087107	T	G	157.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=52.94;MQ0=0;OQ=2398.43;QD=33.78;SB=-1015.12	GT:AD:DP:GL:GQ	1/1:0,71:68:-243.45,-20.48,-0.02:99
+20	10008742	rs12479925	G	T	146.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=35.86;MQ0=1;OQ=685.54;QD=12.24;SB=-274.47	GT:AD:DP:GL:GQ	0/1:26,30:43:-84.79,-12.96,-61.80:99
+20	10008951	.	A	C	553.29	Indel	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=16.13;MQ=51.15;MQ0=0;QD=11.77;SB=-184.92	GT:AD:DP:GL:GQ	0/1:23,24:43:-71.58,-12.97,-70.23:99
+20	10009227	rs12481420	A	G	523.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1201.44;QD=19.70;SB=-625.90	GT:AD:DP:GL:GQ	0/1:22,39:61:-141.80,-18.37,-90.52:99
+20	10009246	rs4574174	A	G	634.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=2711.91;QD=35.68;SB=-1179.49	GT:AD:DP:GL:GQ	1/1:0,76:75:-274.80,-22.59,-0.02:99
+20	10009400	rs6057096	T	A	7.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2788.17;QD=38.19;SB=-1314.62	GT:AD:DP:GL:GQ	1/1:0,73:73:-282.42,-21.98,-0.01:99
+20	10009512	rs6039657	C	G	565.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=3160.94;QD=41.59;SB=-1228.86	GT:AD:DP:GL:GQ	1/1:0,76:74:-319.70,-22.30,-0.02:99
+20	10009719	rs6057097	A	G	58.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.33;MQ0=0;OQ=1551.35;QD=25.02;SB=-585.82	GT:AD:DP:GL:GQ	1/1:0,62:50:-158.78,-15.09,-0.06:99
+20	10009795	rs6118861	A	G	501.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1594.00;QD=35.42;SB=-578.40	GT:AD:DP:GL:GQ	1/1:0,45:45:-163.00,-13.55,-0.01:99
+20	10009844	rs6057098	G	A	11.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.92;MQ=52.80;MQ0=0;OQ=1658.97;QD=30.16;SB=-750.39	GT:AD:DP:GL:GQ	0/1:8,47:51:-184.54,-15.37,-17.54:21.74
+20	10009871	rs6133780	A	G	1067.52	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=16.85;MQ=51.54;MQ0=0;QD=18.09;SB=-387.29	GT:AD:DP:GL:GQ	0/1:19,40:49:-124.80,-14.77,-52.03:99
+20	10009875	rs6133781	A	G	1106.95	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=19.06;MQ=51.21;MQ0=0;QD=19.42;SB=-410.34	GT:AD:DP:GL:GQ	0/1:16,41:44:-127.23,-13.25,-35.68:99
+20	10009879	.	A	G	1218.05	SnpCluster	AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;HRun=1;HaplotypeScore=20.77;MQ=51.40;MQ0=0;QD=23.88;SB=-543.65	GT:AD:DP:GL:GQ	1/1:5,46:42:-136.91,-12.65,-11.59:10.59
+20	10009883	rs6133782	A	G	1399.75	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=11.88;MQ=52.16;MQ0=0;QD=27.45;SB=-484.45	GT:AD:DP:GL:GQ	1/1:2,49:43:-147.73,-12.95,-4.17:87.80
+20	10010393	rs513998	T	G	602.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=1247.20;QD=16.20;SB=-518.70	GT:AD:DP:GL:GQ	0/1:35,42:76:-150.89,-22.89,-128.62:99
+20	10010766	rs517531	T	G	421.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2100.93;QD=31.36;SB=-978.12	GT:AD:DP:GL:GQ	1/1:0,66:67:-217.39,-23.46,-3.72:99
+20	10010832	rs582827	T	C	733.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=2668.46;QD=35.58;SB=-1048.08	GT:AD:DP:GL:GQ	1/1:0,75:75:-270.45,-22.59,-0.02:99
+20	10011075	rs6039659	C	T	234.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=1322.11;QD=15.74;SB=-644.72	GT:AD:DP:GL:GQ	0/1:45,39:82:-160.20,-24.71,-141.60:99
+20	10011309	rs641722	T	C	546.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2396.22;QD=30.72;SB=-1026.41	GT:AD:DP:GL:GQ	1/1:0,78:76:-243.28,-22.92,-0.07:99
+20	10011666	rs546821	C	T	285.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2849.79;QD=40.14;SB=-1187.35	GT:AD:DP:GL:GQ	1/1:0,71:71:-288.58,-21.39,-0.02:99
+20	10011939	rs548863	C	T	181.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=56.14;MQ0=0;OQ=2488.04;QD=39.49;SB=-885.19	GT:AD:DP:GL:GQ	1/1:0,63:62:-252.40,-18.68,-0.01:99
+20	10012362	rs574425	G	T	17.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=51.41;MQ0=0;OQ=676.99;QD=28.21;SB=-89.90	GT:AD:DP:GL:GQ	1/1:0,24:20:-71.29,-6.02,-0.01:60.18
+20	10012384	rs7270107	T	C	128.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=51.62;MQ0=0;OQ=216.13;QD=12.01;SB=-75.35	GT:AD:DP:GL:GQ	0/1:9,9:16:-29.72,-4.82,-34.04:99
+20	10012387	rs6057102	T	C	18.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=50.47;MQ0=0;OQ=295.02;QD=18.44;SB=-77.36	GT:AD:DP:GL:GQ	1/1:0,16:11:-33.10,-3.32,-0.02:33.06
+20	10012479	rs575394	A	G	3.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=49.52;MQ0=0;OQ=474.16;QD=23.71;SB=-247.57	GT:AD:DP:GL:GQ	1/1:0,20:16:-51.02,-4.83,-0.02:48.10
+20	10012498	rs657453	C	G	2.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=40.06;MQ0=0;OQ=331.25;QD=22.08;SB=-84.82	GT:AD:DP:GL:GQ	1/1:0,15:9:-36.71,-2.71,-0.01:27.09
+20	10012518	rs657490	T	C	1.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.64;MQ=34.32;MQ0=0;OQ=366.95;QD=22.93;SB=-197.06	GT:AD:DP:GL:GQ	1/1:0,16:12:-40.29,-3.62,-0.01:36.09
+20	10012521	rs6141099	C	T	33.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=35.97;MQ0=0;OQ=104.02;QD=5.78;SB=-64.27	GT:AD:DP:GL:GQ	0/1:11,7:14:-17.91,-4.23,-28.63:99
+20	10012636	rs57357029	G	C	442.35	Indel	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=46.22;MQ0=1;QD=17.69;SB=-127.71	GT:AD:DP:GL:GQ	0/1:10,15:20:-53.56,-6.04,-26.16:99
+20	10012714	rs577258	G	C	4.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=54.18;MQ0=0;OQ=1374.69;QD=38.19;SB=-268.50	GT:AD:DP:GL:GQ	1/1:0,36:34:-141.07,-10.25,-0.02:99
+20	10012751	rs577383	T	C	3.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=51.17;MQ0=0;OQ=807.71;QD=26.06;SB=-389.47	GT:AD:DP:GL:GQ	1/1:0,31:26:-84.38,-7.84,-0.03:78.14
+20	10013119	rs670350	C	T	14.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=53.67;MQ0=0;OQ=1037.37;QD=17.58;SB=-503.12	GT:AD:DP:GL:GQ	0/1:27,32:57:-124.19,-17.17,-93.21:99
+20	10013574	rs6057108	G	A	190.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.43;MQ0=0;OQ=995.08;QD=15.08;SB=-284.14	GT:AD:DP:GL:GQ	0/1:36,30:66:-122.67,-19.88,-129.26:99
+20	10015679	.	C	T	4.66	PASS	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=130.84;QD=11.89;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,6:10:-19.38,-3.01,-17.14:99
+20	10015761	rs12106014	T	C	188.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=282.39;QD=12.84;SB=-35.94	GT:AD:DP:GL:GQ	0/1:9,13:21:-37.85,-6.33,-34.21:99
+20	10018158	rs512313	G	C	152.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.79;MQ0=0;OQ=1786.48;QD=20.53;SB=-749.98	GT:AD:DP:GL:GQ	0/1:39,47:85:-207.56,-25.63,-151.93:99
+20	10018555	rs570855	G	A	501.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1507.16;QD=18.61;SB=-748.62	GT:AD:DP:GL:GQ	0/1:36,45:80:-178.09,-24.09,-134.36:99
+20	10019093	rs575534	A	G	198.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.34;MQ0=0;OQ=1097.34;QD=15.68;SB=-511.28	GT:AD:DP:GL:GQ	0/1:34,36:69:-133.80,-20.78,-132.32:99
+20	10020229	rs596203	G	A	334.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.76;MQ0=0;OQ=1448.48;QD=18.34;SB=-632.66	GT:AD:DP:GL:GQ	0/1:37,42:79:-171.94,-23.81,-120.12:99
+20	10023689	rs4813909	G	A	153.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.04;MQ0=0;OQ=1887.80;QD=22.74;SB=-948.03	GT:AD:DP:GL:GQ	0/1:30,53:83:-217.06,-25.00,-110.51:99
+20	10024107	.	C	T	114.08	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.56;MQ0=0;OQ=1618.74;QD=19.04;SB=-735.06	GT:AD:DP:GL:GQ	0/1:38,47:84:-190.47,-25.31,-121.49:99
+20	10024288	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=5;HaplotypeScore=7.93;MQ=51.94;MQ0=0;OQ=68.97;QD=0.97;SB=86.23	GT:AD:DP:GL:GQ	0/1:53,18:57:-27.36,-17.18,-167.04:99
+20	10024294	.	C	T	19.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=5;HaplotypeScore=23.45;MQ=49.01;MQ0=1;QD=0.27;SB=83.26	GT:AD:DP:GL:GQ	0/1:55,18:51:-20.62,-15.37,-156.17:52.53
+20	10026357	rs685723	T	C	589.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1010.93;QD=16.57;SB=-474.08	GT:AD:DP:GL:GQ	0/1:26,35:60:-122.45,-18.07,-104.85:99
+20	10026794	rs687514	C	T	152.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1015.27;QD=19.52;SB=-447.00	GT:AD:DP:GL:GQ	0/1:19,32:49:-119.58,-14.77,-61.54:99
+20	10027868	rs514832	A	G	410.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.47;MQ0=0;OQ=1149.09;QD=13.21;SB=-556.55	GT:AD:DP:GL:GQ	0/1:43,44:87:-144.42,-26.22,-173.75:99
+20	10027872	rs594811	A	G	112.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.44;MQ0=0;OQ=1351.31;QD=16.28;SB=-565.56	GT:AD:DP:GL:GQ	0/1:39,44:83:-163.41,-25.00,-161.96:99
+20	10030188	rs652633	T	A	473.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.71;MQ0=0;OQ=1186.53;QD=15.02;SB=-453.42	GT:AD:DP:GL:GQ	0/1:41,38:79:-145.73,-23.79,-157.38:99
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+20	10031798	rs669985	G	A	353.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=4247.21;QD=40.84;SB=-1915.55	GT:AD:DP:GL:GQ	1/1:0,104:104:-423.72,-31.33,-0.03:99
+20	10031827	rs558493	C	T	27.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.83;MQ0=0;OQ=1957.26;QD=18.12;SB=-1004.58	GT:AD:DP:GL:GQ	0/1:52,56:108:-231.54,-32.53,-189.42:99
+20	10032094	rs681750	G	A	562.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.21;QD=14.16;SB=-575.44	GT:AD:DP:GL:GQ	0/1:47,36:82:-145.51,-24.71,-151.92:99
+20	10032413	rs683145	T	G	535.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=698.84;QD=11.09;SB=-317.98	GT:AD:DP:GL:GQ	0/1:33,30:63:-92.15,-18.98,-124.49:99
+20	10032882	rs479039	A	T	24.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=0;HaplotypeScore=7.14;MQ=58.99;MQ0=0;OQ=1029.41;QD=13.73;SB=-439.55	GT:AD:DP:GL:GQ	0/1:40,34:73:-128.21,-21.99,-155.80:99
+20	10034306	rs604452	T	C	170.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.46;MQ0=0;OQ=667.43;QD=8.67;SB=-359.16	GT:AD:DP:GL:GQ	0/1:47,29:73:-92.02,-22.00,-181.63:99
+20	10037037	rs2327261	C	T	271.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.97;MQ0=0;OQ=1384.69;QD=17.53;SB=-468.51	GT:AD:DP:GL:GQ	0/1:38,41:74:-164.05,-22.30,-111.89:99
+20	10037709	rs518364	A	T	403.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.68;MQ0=0;OQ=896.68;QD=12.63;SB=-381.55	GT:AD:DP:GL:GQ	0/1:39,32:70:-114.04,-21.09,-148.36:99
+20	10039371	rs678696	T	G	586.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1105.57;QD=15.79;SB=-406.66	GT:AD:DP:GL:GQ	0/1:32,38:70:-134.92,-21.08,-120.34:99
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+20	10043002	.	A	T	147.57	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1103.68;QD=13.14;SB=-535.28	GT:AD:DP:GL:GQ	0/1:48,36:84:-138.95,-25.30,-175.62:99
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+20	10045078	rs674630	G	T	86.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=58.99;MQ0=0;OQ=2874.89;QD=36.39;SB=-1368.13	GT:AD:DP:GL:GQ	1/1:0,79:78:-291.09,-23.49,-0.02:99
+20	10045642	rs572752	G	C	658.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3374.18;QD=42.18;SB=-1455.16	GT:AD:DP:GL:GQ	1/1:0,80:79:-336.42,-23.81,-0.03:99
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+20	10050828	rs660454	T	C	314.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.73;MQ0=0;OQ=1072.85;QD=12.62;SB=-513.86	GT:AD:DP:GL:GQ	0/1:48,37:84:-135.87,-25.30,-193.36:99
+20	10051448	rs565455	T	C	358.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.41;MQ0=0;OQ=1005.69;QD=14.16;SB=-400.33	GT:AD:DP:GL:GQ	0/1:36,35:69:-124.64,-20.79,-133.98:99
+20	10052688	.	C	A	247.91	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=928.77;QD=12.06;SB=-460.78	GT:AD:DP:GL:GQ	0/1:45,32:77:-119.35,-23.19,-165.26:99
+20	10058022	rs531797	T	C	82.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=6.22;MQ=58.46;MQ0=0;OQ=872.91;QD=12.47;SB=-339.92	GT:AD:DP:GL:GQ	0/1:38,32:67:-110.76,-20.18,-144.54:99
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+20	10067264	rs530271	G	A	217.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.68;MQ0=0;OQ=2865.42;QD=39.80;SB=-1324.28	GT:AD:DP:GL:GQ	1/1:0,72:72:-290.15,-21.69,-0.02:99
+20	10067722	rs604416	A	C	278.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1822.34;QD=35.05;SB=-862.09	GT:AD:DP:GL:GQ	1/1:0,52:52:-185.83,-15.66,-0.02:99
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+20	10070602	rs6039684	T	C	187.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.71;MQ0=0;OQ=2364.76;QD=32.84;SB=-1139.10	GT:AD:DP:GL:GQ	1/1:0,72:69:-240.09,-20.79,-0.03:99
+20	10070936	.	T	A	3050.87	Indel	AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=58.76;MQ0=0;QD=37.67;SB=-1399.42	GT:AD:DP:GL:GQ	1/1:0,81:80:-308.69,-24.09,-0.02:99
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+20	10071890	rs6039685	T	C	547.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1748.72;QD=30.68;SB=-861.55	GT:AD:DP:GL:GQ	1/1:0,57:56:-178.51,-16.89,-0.05:99
+20	10072505	rs6032786	A	G	465.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1789.94;QD=28.41;SB=-916.44	GT:AD:DP:GL:GQ	1/1:0,63:57:-182.63,-17.19,-0.05:99
+20	10074187	.	A	G	68.82	PASS	AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2702.25;QD=35.09;SB=-1331.57	GT:AD:DP:GL:GQ	1/1:0,77:77:-273.84,-23.20,-0.03:99
+20	10074240	rs614270	T	C	574.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2989.29;QD=34.76;SB=-1439.46	GT:AD:DP:GL:GQ	1/1:0,85:83:-302.53,-25.00,-0.02:99
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+20	10077752	.	T	C	195.33	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1175.95;QD=14.89;SB=-463.61	GT:AD:DP:GL:GQ	0/1:34,45:79:-144.69,-23.81,-137.94:99
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+20	10081800	rs474169	C	T	600.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.62;QD=16.25;SB=-544.01	GT:AD:DP:GL:GQ	0/1:34,33:67:-132.33,-20.18,-122.19:99
+20	10082892	rs644145	C	T	208.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1601.32;QD=38.13;SB=-762.50	GT:AD:DP:GL:GQ	1/1:0,42:41:-163.73,-12.35,-0.01:99
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+20	10087394	rs608188	T	G	410.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=1428.70;QD=17.21;SB=-695.70	GT:AD:DP:GL:GQ	0/1:35,48:83:-171.15,-25.00,-131.95:99
+20	10087754	rs544718	T	G	209.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=60.45;MQ0=0;OQ=1195.66;QD=15.33;SB=-504.83	GT:AD:DP:GL:GQ	0/1:36,42:77:-146.04,-23.19,-131.14:99
+20	10087804	rs609932	C	T	337.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=60.49;MQ0=0;OQ=1534.51;QD=15.35;SB=-666.41	GT:AD:DP:GL:GQ	0/1:50,50:93:-184.76,-28.03,-153.45:99
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+20	10088736	rs624401	A	C	166.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=51.41;MQ0=0;OQ=755.82;QD=12.81;SB=-289.77	GT:AD:DP:GL:GQ	0/1:29,29:53:-94.83,-15.97,-94.03:99
+20	10088747	rs624419	A	G	458.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=732.27;QD=13.31;SB=-319.26	GT:AD:DP:GL:GQ	0/1:25,30:54:-92.79,-16.28,-99.03:99
+20	10088799	rs624824	G	A	1.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.24;MQ0=0;OQ=1015.57;QD=18.46;SB=-384.14	GT:AD:DP:GL:GQ	0/1:24,31:54:-121.12,-16.28,-76.29:99
+20	10088895	rs500269	C	T	289	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.39;MQ0=0;OQ=522.39;QD=12.74;SB=-237.72	GT:AD:DP:GL:GQ	0/1:24,17:39:-67.28,-11.76,-70.34:99
+20	10088985	rs2876185	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=28.26;MQ=49.95;MQ0=0;OQ=805.93;QD=10.20;SB=-330.82	GT:AD:DP:GL:GQ	0/1:43,35:73:-105.88,-22.00,-156.93:99
+20	10089441	rs637625	A	G	358.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=992.46;QD=13.23;SB=-330.00	GT:AD:DP:GL:GQ	0/1:37,38:73:-124.53,-22.00,-148.03:99
+20	10089525	rs526819	C	T	411.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.84;MQ0=0;OQ=1526.59;QD=17.96;SB=-694.71	GT:AD:DP:GL:GQ	0/1:41,44:82:-180.66,-24.71,-123.55:99
+20	10090764	rs670562	A	G	90.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=59.44;MQ0=0;OQ=705.16;QD=10.52;SB=-326.14	GT:AD:DP:GL:GQ	0/1:37,30:65:-93.39,-19.59,-148.34:99
+20	10090970	rs671426	T	C	386.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.73;MQ0=0;OQ=1093.51;QD=15.62;SB=-550.11	GT:AD:DP:GL:GQ	0/1:33,37:67:-132.81,-20.18,-125.76:99
+20	10091214	rs563455	C	T	321.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.75;MQ0=0;OQ=1276.23;QD=17.02;SB=-480.51	GT:AD:DP:GL:GQ	0/1:36,39:73:-152.90,-21.99,-128.97:99
+20	10092415	rs590717	A	G	409.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1457.26;QD=14.57;SB=-743.58	GT:AD:DP:GL:GQ	0/1:51,49:100:-179.13,-30.12,-213.26:99
+20	10092927	.	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=8.09;MQ=59.09;MQ0=0;OQ=102.52;QD=1.35;SB=110.34	GT:AD:DP:GL:GQ	0/1:58,17:57:-30.71,-17.17,-163.94:99
+20	10093923	rs2423481	T	A	501.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=952.53;QD=14.65;SB=-490.92	GT:AD:DP:GL:GQ	0/1:33,32:64:-117.81,-19.28,-126.25:99
+20	10094251	rs543895	T	A	466.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.29;QD=18.66;SB=-397.80	GT:AD:DP:GL:GQ	0/1:26,37:59:-138.58,-17.77,-89.00:99
+20	10094582	rs56124148	A	G	315.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.72;MQ0=0;OQ=736.10;QD=11.15;SB=-314.87	GT:AD:DP:GL:GQ	0/1:38,28:65:-96.47,-19.58,-152.04:99
+20	10094774	rs570383	C	T	361.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=1017.49;QD=13.75;SB=-374.10	GT:AD:DP:GL:GQ	0/1:39,35:69:-125.82,-20.79,-130.93:99
+20	10095741	rs489548	A	G	80.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=57.01;MQ0=0;OQ=943.34;QD=13.29;SB=-405.22	GT:AD:DP:GL:GQ	0/1:36,34:68:-118.10,-20.48,-142.28:99
+20	10096293	rs515940	C	T	94.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.19;MQ0=0;OQ=1320.58;QD=17.61;SB=-665.71	GT:AD:DP:GL:GQ	0/1:37,38:74:-157.63,-22.29,-130.19:99
+20	10096596	rs518701	C	T	23.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.03;MQ0=0;OQ=1543.46;QD=17.95;SB=-788.95	GT:AD:DP:GL:GQ	0/1:40,46:85:-183.24,-25.61,-136.84:99
+20	10096768	rs520453	A	C	398.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1343.01;QD=15.44;SB=-695.73	GT:AD:DP:GL:GQ	0/1:42,45:87:-163.78,-26.20,-154.89:99
+20	10096899	rs652086	G	T	1162.66	Indel	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.76;MQ0=0;QD=14.72;SB=-335.13	GT:AD:DP:GL:GQ	0/1:39,40:78:-143.04,-23.49,-142.37:99
+20	10096933	rs652126	G	C	307.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1416.78;QD=16.87;SB=-379.18	GT:AD:DP:GL:GQ	0/1:45,39:83:-169.97,-25.01,-193.85:99
+20	10096958	rs652494	G	A	342.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.79;MQ0=0;OQ=1501.31;QD=16.68;SB=-462.96	GT:AD:DP:GL:GQ	0/1:45,45:87:-179.62,-26.20,-157.70:99
+20	10097075	rs6077657	T	G	299.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=1264.80;QD=13.75;SB=-586.94	GT:AD:DP:GL:GQ	0/1:44,48:90:-156.87,-27.11,-157.64:99
+20	10097437	rs11698147	T	C	519.38	Indel	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.01;HRun=1;HaplotypeScore=8.62;MQ=55.90;MQ0=0;QD=7.75;SB=-133.24	GT:AD:DP:GL:GQ	0/1:45,21:62:-73.60,-18.38,-162.59:99
+20	10097465	.	C	T	31.87	LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=3;HaplotypeScore=12.58;MQ=57.18;MQ0=0;QD=0.61;SB=-33.97	GT:AD:DP:GL:GQ	0/1:46,5:49:-20.93,-14.46,-150.67:64.70
+20	10097626	rs665397	C	A	205.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.09;MQ0=0;OQ=521.22;QD=11.33;SB=-241.94	GT:AD:DP:GL:GQ	0/1:27,19:45:-68.96,-13.55,-93.68:99
+20	10097789	rs550824	T	C	40.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.80;MQ=57.53;MQ0=1;OQ=609.05;QD=10.15;SB=-279.29	GT:AD:DP:GL:GQ	0/1:35,25:57:-81.36,-17.17,-136.53:99
+20	10097928	rs666732	G	A	147.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.09;MQ0=0;OQ=647.39;QD=16.60;SB=-318.83	GT:AD:DP:GL:GQ	0/1:17,22:38:-79.48,-11.45,-61.53:99
+20	10098110	rs6108402	G	C	43.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=639.58;QD=17.77;SB=-86.92	GT:AD:DP:GL:GQ	0/1:19,17:35:-77.79,-10.55,-73.75:99
+20	10098135	rs6108403	C	A	5.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.93;MQ0=0;OQ=389.51;QD=10.25;SB=-43.38	GT:AD:DP:GL:GQ	0/1:24,14:38:-53.68,-11.44,-83.52:99
+20	10098237	.	A	T	39.55	PASS	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.32;MQ0=0;OQ=159.94;QD=12.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,6:13:-23.19,-3.92,-25.88:99
+20	10098265	.	T	C	37.58	PASS	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.10;MQ0=0;OQ=64.00;QD=12.80;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,3:5:-11.19,-1.51,-7.23:57.28
+20	10098344	.	A	G	24.50	LowQual	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=6.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,2:4:-6.94,-1.20,-8.11:57.33
+20	10098786	.	C	T	16.33	LowQual	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=54.65;MQ0=0;QD=1.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,2:9:-7.62,-2.71,-21.38:49.06
+20	10098945	rs56176249	T	C	5.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=51.33;MQ0=0;OQ=363.84;QD=17.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,13:20:-45.69,-6.02,-27.59:99
+20	10098987	.	C	T	11	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.90;MQ0=0;OQ=342.06;QD=14.87;SB=-3.99	GT:AD:DP:GL:GQ	0/1:10,13:21:-43.82,-6.33,-33.84:99
+20	10099029	rs13044987	T	C	3.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.87;MQ0=0;OQ=125.69;QD=4.66;SB=2.03	GT:AD:DP:GL:GQ	0/1:18,9:25:-23.39,-7.53,-70.35:99
+20	10099034	rs13043768	C	A	139.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.19;MQ0=0;OQ=176.63;QD=6.31;SB=-31.94	GT:AD:DP:GL:GQ	0/1:18,10:26:-28.78,-7.84,-59.75:99
+20	10099044	rs13043626	A	C	29.61	LowQual	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=51.36;MQ0=0;QD=1.29;SB=-14.48	GT:AD:DP:GL:GQ	0/1:16,7:15:-10.76,-4.52,-43.68:62.44
+20	10099055	rs13045001	T	C	65.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=48.67;MQ0=0;OQ=222.63;QD=7.95;SB=-64.86	GT:AD:DP:GL:GQ	0/1:16,12:23:-32.47,-6.93,-57.23:99
+20	10099079	rs13043786	C	T	16.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=5.99;MQ=49.66;MQ0=0;OQ=370.70;QD=10.59;SB=-162.25	GT:AD:DP:GL:GQ	0/1:21,14:31:-49.70,-9.35,-56.03:99
+20	10099140	rs585009	G	T	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=2.65;MQ=55.73;MQ0=0;OQ=847.58;QD=14.13;SB=-233.91	GT:AD:DP:GL:GQ	0/1:30,30:58:-105.51,-17.47,-102.15:99
+20	10099190	rs508242	G	T	210.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.42;MQ0=0;OQ=860.99;QD=13.25;SB=-270.28	GT:AD:DP:GL:GQ	0/1:33,32:62:-108.05,-18.67,-118.91:99
+20	10099220	rs585404	A	G	5.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=6.00;MQ=56.96;MQ0=0;OQ=481.07;QD=10.46;SB=-187.61	GT:AD:DP:GL:GQ	0/1:25,21:43:-64.35,-12.96,-100.07:99
+20	10099250	rs585439	G	A	100.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=56.23;MQ0=0;OQ=672.67;QD=17.70;SB=-330.34	GT:AD:DP:GL:GQ	0/1:17,21:36:-81.41,-10.86,-48.14:99
+20	10099535	rs586791	G	A	209.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.28;MQ0=0;OQ=1326.40;QD=20.73;SB=-582.88	GT:AD:DP:GL:GQ	0/1:25,38:62:-157.48,-21.55,-76.17:99
+20	10099565	rs532882	C	T	44.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.99;MQ=59.66;MQ0=0;OQ=1282.88;QD=19.15;SB=-617.46	GT:AD:DP:GL:GQ	0/1:30,37:67:-151.75,-20.18,-103.68:99
+20	10099755	rs534687	C	T	66.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=1091.00;QD=16.78;SB=-547.75	GT:AD:DP:GL:GQ	0/1:32,33:64:-131.66,-19.27,-116.96:99
+20	10099832	rs534882	A	G	477.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=927.85;QD=12.89;SB=-445.10	GT:AD:DP:GL:GQ	0/1:39,33:71:-117.45,-21.39,-156.97:99

public/testdata/VariantEval/header.txt

@@ -0,0 +1,14 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625

public/testdata/VariantEval/indbnp129_notindbsnp132.txt

@@ -0,0 +1 @@
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37

public/testdata/VariantEval/indbnp132_notindbsnp129.txt

@@ -0,0 +1,2 @@
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.

public/testdata/VariantEval/indels.txt

@@ -0,0 +1 @@
+20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	.	AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338

public/testdata/VariantEval/inhapmap.txt

@@ -0,0 +1 @@
+20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/VariantEval/inomni.txt

@@ -0,0 +1 @@
+20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182

public/testdata/VariantEval/missense.txt

@@ -0,0 +1 @@
+20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144

public/testdata/VariantEval/one_transition_and_one_transversion.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0

public/testdata/VariantEval/pacbio.hg19.intervals

@@ -0,0 +1,61 @@
+20:1408612-1410111
+20:2156456-2157954
+20:2449737-2451239
+20:3152386-3153891
+20:4756022-4757518
+20:5904863-5906362
+20:6229017-6230516
+20:6348326-6349839
+20:6468951-6470450
+20:8669911-8671404
+20:9090417-9091931
+20:10339474-10340969
+20:11964411-11965911
+20:12189566-12191074
+20:15237801-15239305
+20:15965572-15967061
+20:16075651-16077128
+20:16990896-16992393
+20:23364965-23366475
+20:23710044-23711543
+20:23773906-23775416
+20:24317459-24318954
+20:25830118-25831610
+20:25890727-25892236
+20:25904830-25906332
+20:26130086-26133738
+20:26142111-26144870
+20:26145383-26146891
+20:26148300-26149799
+20:26207333-26208839
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public/testdata/VariantEval/pacbio.ts.recalibrated.vcf

@@ -0,0 +1,566 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="log10-scaled probability of variant being true under the trained gaussian mixture model">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.recal.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/Q-27737@node1309-1-sg/temp-1/scatter.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.rod downsampling_type=null downsample_to_fraction=null downsample_to_coverage=250 baq=RECALCULATE baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=NA12878 min_base_quality_score=10 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.5 get_indel_alleles_from_vcf=false min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub verbose_mode=null metrics_file=null annotation=[]"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/Q-27737@node1309-2-sg/temp-1/scatter.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.raw.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1] filterName=[HARD_TO_VALIDATE] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
+##VariantRecalibrator="analysis_type=VariantRecalibrator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf, /humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.filtered.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.rod downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false cluster_file=/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.clusters tranches_file=/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.ts.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub target_titv=1.8 backOff=1.3 ignore_all_input_filters=false priorNovel=2.0 priorDBSNP=2.0 priorHapMap=2.0 prior1KG=2.0 path_to_Rscript=Rscript path_to_resources=R/ singleton_fp_rate=0.5 max_ac_prior=0.99 dontTrustACField=false qual=0.0 debugFile=null selectionMetric=TRUTH_SENSITIVITY use_annotation=null"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	1408919	rs6074626	C	T	410.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.06;HRun=1;HaplotypeScore=114.0668;MQ=60.00;MQ0=0;QD=5.33;SB=-173.00;VQSLOD=-1.3245;sumGLbyD=5.72	GT:AD:DP:GQ:PL	0/1:41,29:58:99:440,0,594
+20	1409435	rs4814243	G	A	2219.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=175;Dels=0.01;HRun=0;HaplotypeScore=161.5624;MQ=60.00;MQ0=0;QD=12.68;SB=-808.23;VQSLOD=-2.4575;sumGLbyD=12.87	GT:AD:DP:GQ:PL	1/1:9,139:109:99:2252,161,0
+20	1409567	rs4814244	A	G	1734.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=153;Dels=0.22;HRun=1;HaplotypeScore=505.1471;MQ=60.00;MQ0=0;QD=11.33;SB=-772.45;VQSLOD=-1.6321;sumGLbyD=11.55	GT:AD:DP:GQ:PL	1/1:6,111:82:99:1767,193,0
+20	1409612	.	T	A	579.26	PASS	AC=1;AF=0.50;AN=2;DP=148;Dels=0.16;HRun=2;HaplotypeScore=372.8065;MQ=60.00;MQ0=0;QD=3.91;SB=-155.28;VQSLOD=-2.1200;sumGLbyD=4.12	GT:AD:DP:GQ:PL	0/1:74,45:87:99:609,0,883
+20	1409757	rs6134916	C	T	252.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.08;HRun=1;HaplotypeScore=176.9395;MQ=60.00;MQ0=0;QD=2.77;SB=-123.36;VQSLOD=-1.3707;sumGLbyD=3.10	GT:AD:DP:GQ:PL	0/1:54,24:58:99:282,0,673
+20	2156688	rs34950074	A	G	160.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.20;HRun=3;HaplotypeScore=311.7372;MQ=60.00;MQ0=0;QD=1.98;SB=-59.56;VQSLOD=-3.8407;sumGLbyD=2.35	GT:AD:DP:GQ:PL	0/1:41,19:52:99:191,0,699
+20	2157130	rs6137228	G	A	1074.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=241;Dels=0.08;HRun=0;HaplotypeScore=495.1212;MQ=60.00;MQ0=0;QD=4.46;SB=-543.36;VQSLOD=-1.0631;sumGLbyD=4.58	GT:AD:DP:GQ:PL	0/1:129,88:161:99:1105,0,1376
+20	2157596	rs41308621	G	A	37.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=115;Dels=0.16;HRun=0;HaplotypeScore=356.4928;MQ=60.00;MQ0=0;QD=0.33;SB=7.11;VQSLOD=-2.1065;sumGLbyD=0.59	GT:AD:DP:GQ:PL	0/1:67,29:45:67.65:68,0,574
+20	2450144	rs6106763	T	C	384.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=161;Dels=0.09;HRun=1;HaplotypeScore=350.4436;MQ=60.00;MQ0=0;QD=2.39;SB=-164.46;VQSLOD=-1.2122;sumGLbyD=2.57	GT:AD:DP:GQ:PL	0/1:93,48:111:99:414,0,1456
+20	2450235	rs6138180	A	T	646.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=211;Dels=0.14;HRun=0;HaplotypeScore=566.4039;MQ=60.00;MQ0=0;QD=3.06;SB=-286.95;VQSLOD=-1.6466;sumGLbyD=3.21	GT:AD:DP:GQ:PL	0/1:105,68:127:99:677,0,1540
+20	2450669	rs6049283	C	A	859.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=213;DS;Dels=0.00;HRun=0;HaplotypeScore=268.1049;MQ=60.00;MQ0=0;QD=4.04;SB=-396.35;VQSLOD=-0.4104;sumGLbyD=4.18	GT:AD:DP:GQ:PL	0/1:124,78:126:99:890,0,1027
+20	3152793	rs6051617	T	C	196.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.02;HRun=0;HaplotypeScore=156.2935;MQ=60.00;MQ0=0;QD=1.93;SB=-54.81;VQSLOD=-1.0530;sumGLbyD=2.22	GT:AD:DP:GQ:PL	0/1:71,25:74:99:227,0,1001
+20	3153236	.	C	G	304.30	PASS	AC=1;AF=0.50;AN=2;DP=119;Dels=0.16;HRun=1;HaplotypeScore=320.3893;MQ=60.00;MQ0=0;QD=2.56;SB=-155.71;VQSLOD=-1.3115;sumGLbyD=2.81	GT:AD:DP:GQ:PL	0/1:63,30:69:99:334,0,819
+20	3153503	rs55785911	G	A	88.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.11;HRun=1;HaplotypeScore=160.1451;MQ=60.00;MQ0=0;QD=1.23;SB=-51.31;VQSLOD=-2.1979;sumGLbyD=1.65	GT:AD:DP:GQ:PL	0/1:44,18:42:99:119,0,606
+20	3153605	.	C	T	151.39	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.15;HRun=1;HaplotypeScore=161.0277;MQ=60.00;MQ0=0;QD=2.52;SB=-20.11;VQSLOD=-2.1881;sumGLbyD=3.02	GT:AD:DP:GQ:PL	0/1:31,19:32:99:181,0,388
+20	4756391	rs2422967	T	C	266.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=177;Dels=0.15;HRun=3;HaplotypeScore=562.1195;MQ=60.00;MQ0=0;QD=1.51;SB=-15.41;VQSLOD=-5.2491;sumGLbyD=1.67	GT:AD:DP:GQ:PL	0/1:112,33:115:99:296,0,1675
+20	4756509	rs6052868	A	G	509.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=250;DS;Dels=0.17;HRun=3;HaplotypeScore=748.4880;MQ=60.00;MQ0=0;QD=2.04;SB=-264.37;VQSLOD=-2.4325;sumGLbyD=2.16	GT:AD:DP:GQ:PL	0/1:153,49:168:99:539,0,2447
+20	4756691	rs7272323	G	C	624.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.00;HRun=0;HaplotypeScore=196.5430;MQ=60.00;MQ0=0;QD=2.52;SB=-163.80;VQSLOD=-0.2919;sumGLbyD=2.64	GT:AD:DP:GQ:PL	0/1:175,68:164:99:655,0,1886
+20	5905472	rs236154	G	T	764.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.00;HRun=0;HaplotypeScore=202.1957;MQ=60.00;MQ0=0;QD=4.23;SB=-330.33;VQSLOD=-0.4780;sumGLbyD=4.39	GT:AD:DP:GQ:PL	0/1:111,68:100:99:795,0,873
+20	5905550	rs236155	G	A	1050.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.02;HRun=0;HaplotypeScore=173.3788;MQ=60.00;MQ0=0;QD=6.14;SB=-462.20;VQSLOD=-1.2994;sumGLbyD=6.32	GT:AD:DP:GQ:PL	0/1:79,82:131:99:1080,0,1181
+20	5905779	rs2821	C	A	550.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=158;Dels=0.05;HRun=0;HaplotypeScore=266.6426;MQ=60.00;MQ0=0;QD=3.48;SB=-201.81;VQSLOD=-0.4809;sumGLbyD=3.67	GT:AD:DP:GQ:PL	0/1:90,51:108:99:580,0,1342
+20	5906092	rs236157	G	A	195.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.04;HRun=0;HaplotypeScore=129.6758;MQ=60.00;MQ0=0;QD=2.76;SB=-84.66;VQSLOD=-0.6734;sumGLbyD=3.18	GT:AD:DP:GQ:PL	0/1:39,25:45:99:226,0,542
+20	5906098	rs10454160	A	C	79.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.13;HRun=0;HaplotypeScore=191.3074;MQ=60.00;MQ0=0;QD=1.14;SB=15.70;VQSLOD=-1.8202;sumGLbyD=1.57	GT:AD:DP:GQ:PL	0/1:42,17:45:99:110,0,679
+20	6229263	rs6054023	T	C	393.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.05;HRun=0;HaplotypeScore=143.3775;MQ=60.00;MQ0=0;QD=3.86;SB=-117.41;VQSLOD=-0.4836;sumGLbyD=4.15	GT:AD:DP:GQ:PL	0/1:64,31:77:99:424,0,859
+20	6229282	rs6054024	A	C	276.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.11;HRun=0;HaplotypeScore=239.9223;MQ=60.00;MQ0=0;QD=2.71;SB=-129.32;VQSLOD=-0.4773;sumGLbyD=3.01	GT:AD:DP:GQ:PL	0/1:58,27:65:99:307,0,790
+20	6229367	rs55708193	C	A	284.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=100.3668;MQ=60.00;MQ0=0;QD=2.46;SB=9.48;VQSLOD=-1.8120;sumGLbyD=2.71	GT:AD:DP:GQ:PL	0/1:75,31:76:99:315,0,984
+20	6229867	rs6054027	C	A	1024.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=224;Dels=0.04;HRun=0;HaplotypeScore=254.7872;MQ=60.00;MQ0=0;QD=4.57;SB=-449.69;VQSLOD=-0.6894;sumGLbyD=4.71	GT:AD:DP:GQ:PL	0/1:120,90:160:99:1054,0,1742
+20	6230133	rs6038393	C	T	271.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=142;Dels=0.00;HRun=0;HaplotypeScore=102.9663;MQ=60.00;MQ0=0;QD=1.91;SB=-85.43;VQSLOD=-1.2156;sumGLbyD=2.12	GT:AD:DP:GQ:PL	0/1:95,43:79:99:302,0,1065
+20	6230247	rs6085447	T	A	341.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.04;HRun=2;HaplotypeScore=109.4730;MQ=60.00;MQ0=0;QD=3.49;SB=-99.61;VQSLOD=-2.3533;sumGLbyD=3.79	GT:AD:DP:GQ:PL	0/1:51,39:62:99:372,0,694
+20	6469312	rs4441551	C	G	323.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.11;HRun=1;HaplotypeScore=193.6133;MQ=60.00;MQ0=0;QD=3.63;SB=-89.68;VQSLOD=-1.4989;sumGLbyD=3.97	GT:AD:DP:GQ:PL	0/1:49,28:70:99:353,0,833
+20	6469515	rs62200027	G	A	808.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.03;HRun=0;HaplotypeScore=175.1223;MQ=60.00;MQ0=0;QD=4.35;SB=-356.55;VQSLOD=-0.6362;sumGLbyD=4.51	GT:AD:DP:GQ:PL	0/1:104,67:137:99:839,0,1240
+20	6469596	rs17721822	G	A	895.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;Dels=0.00;HRun=0;HaplotypeScore=197.3459;MQ=60.00;MQ0=0;QD=4.22;SB=-354.06;VQSLOD=-0.5273;sumGLbyD=4.37	GT:AD:DP:GQ:PL	0/1:126,80:147:99:926,0,1588
+20	6470035	rs928203	T	C	414.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=130;Dels=0.00;HRun=0;HaplotypeScore=127.3479;MQ=60.00;MQ0=0;QD=3.19;SB=-135.40;VQSLOD=-0.3583;sumGLbyD=3.42	GT:AD:DP:GQ:PL	0/1:74,43:77:99:445,0,890
+20	6470094	rs2326788	G	A	478.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.01;HRun=0;HaplotypeScore=94.4097;MQ=60.00;MQ0=0;QD=4.23;SB=-145.71;VQSLOD=-0.5743;sumGLbyD=4.50	GT:AD:DP:GQ:PL	0/1:60,44:69:99:508,0,506
+20	6470104	rs2326789	G	A	358.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.03;HRun=0;HaplotypeScore=119.9128;MQ=60.00;MQ0=0;QD=3.23;SB=-119.02;VQSLOD=-0.4560;sumGLbyD=3.50	GT:AD:DP:GQ:PL	0/1:61,41:69:99:389,0,613
+20	6470265	rs928202	A	G	225.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.18;HRun=2;HaplotypeScore=279.3012;MQ=60.00;MQ0=0;QD=2.66;SB=-42.82;VQSLOD=-2.0778;sumGLbyD=3.01	GT:AD:DP:GQ:PL	0/1:44,21:53:99:256,0,596
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+20	26131748	.	T	C	88.77	PASS	AC=1;AF=0.50;AN=2;DP=103;Dels=0.08;HRun=0;HaplotypeScore=180.3277;MQ=60.00;MQ0=0;QD=0.86;SB=-37.87;VQSLOD=-1.6056;sumGLbyD=1.15	GT:AD:DP:GQ:PL	0/1:69,24:55:99:119,0,810
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+20	26131777	.	T	C	80.43	PASS	AC=1;AF=0.50;AN=2;DP=92;Dels=0.08;HRun=0;HaplotypeScore=152.2912;MQ=60.00;MQ0=0;QD=0.87;SB=-36.93;VQSLOD=-1.7622;sumGLbyD=1.20	GT:AD:DP:GQ:PL	0/1:69,15:44:99:110,0,609
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+20	26131879	.	T	C	87.62	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.02;HRun=0;HaplotypeScore=39.1091;MQ=60.00;MQ0=0;QD=1.75;SB=-29.20;VQSLOD=-2.3968;sumGLbyD=2.35	GT:AD:DP:GQ:PL	0/1:37,11:33:99:118,0,452
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+20	26207975	.	T	C	1009.54	PASS	AC=1;AF=0.50;AN=2;DP=160;Dels=0.18;HRun=1;HaplotypeScore=548.6023;MQ=60.00;MQ0=0;QD=6.31;SB=-505.03;VQSLOD=-3.8476;sumGLbyD=6.50	GT:AD:DP:GQ:PL	0/1:60,65:98:99:1040,0,659
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+20	26208024	.	C	T	1277.75	PASS	AC=1;AF=0.50;AN=2;DP=162;Dels=0.06;HRun=0;HaplotypeScore=352.1320;MQ=60.00;MQ0=0;QD=7.89;SB=-634.68;VQSLOD=-2.7244;sumGLbyD=8.07	GT:AD:DP:GQ:PL	0/1:52,98:112:99:1308,0,619
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+20	29435660	rs13045968	A	G	322.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.19;HRun=1;HaplotypeScore=115.5873;MQ=60.00;MQ0=0;QD=7.49;SB=-72.77;VQSLOD=-1.9071;sumGLbyD=8.19	GT:AD:DP:GQ:PL	0/1:12,21:27:88.09:352,0,88
+20	29435686	rs13036813	T	C	188.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.07;HRun=0;HaplotypeScore=79.2513;MQ=60.00;MQ0=0;QD=4.09;SB=-81.50;VQSLOD=-1.0253;sumGLbyD=4.74	GT:AD:DP:GQ:PL	0/1:20,22:30:99:218,0,242
+20	29435702	rs13036824	T	G	70.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=34.6042;MQ=60.00;MQ0=0;QD=1.47;SB=-16.52;VQSLOD=-3.3206;sumGLbyD=2.10	GT:AD:DP:GQ:PL	0/1:35,13:36:99:101,0,514
+20	29435746	rs13044090	C	T	316.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.06;HRun=0;HaplotypeScore=70.6853;MQ=60.00;MQ0=0;QD=6.32;SB=-59.82;VQSLOD=-1.9571;sumGLbyD=6.92	GT:AD:DP:GQ:PL	0/1:17,27:34:99:346,0,253
+20	29435832	rs13040301	G	A	239.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.08;HRun=1;HaplotypeScore=104.9138;MQ=60.00;MQ0=0;QD=4.07;SB=-104.52;VQSLOD=-1.7950;sumGLbyD=4.57	GT:AD:DP:GQ:PL	0/1:26,21:45:99:270,0,473
+20	29435854	rs13040308	G	T	133.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.05;HRun=0;HaplotypeScore=51.7621;MQ=60.00;MQ0=0;QD=2.09;SB=-42.73;VQSLOD=-1.9053;sumGLbyD=2.55	GT:AD:DP:GQ:PL	0/1:42,16:50:99:163,0,714
+20	29435887	rs13037177	T	C	286.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=0;HaplotypeScore=71.2934;MQ=60.00;MQ0=0;QD=4.34;SB=-84.18;VQSLOD=-1.1350;sumGLbyD=4.79	GT:AD:DP:GQ:PL	0/1:33,26:48:99:316,0,442
+20	29435941	rs13037204	T	C	146.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=69.6146;MQ=60.00;MQ0=0;QD=2.19;SB=-54.89;VQSLOD=-1.5516;sumGLbyD=2.64	GT:AD:DP:GQ:PL	0/1:50,16:29:99:177,0,315
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+20	29436082	.	C	T	35.69	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=2;HaplotypeScore=61.3692;MQ=60.00;MQ0=0;QD=0.49;SB=-23.15;VQSLOD=-4.1195;sumGLbyD=0.90	GT:AD:DP:GQ:PL	0/1:58,14:46:65.68:66,0,715
+20	29436086	.	C	A	86.37	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=84.7886;MQ=60.00;MQ0=0;QD=1.18;SB=-49.81;VQSLOD=-2.1138;sumGLbyD=1.59	GT:AD:DP:GQ:PL	0/1:51,17:44:99:116,0,613
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+20	29436239	rs4010657	T	C	159.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.06;HRun=0;HaplotypeScore=92.7959;MQ=60.00;MQ0=0;QD=3.01;SB=-93.08;VQSLOD=-0.7822;sumGLbyD=3.58	GT:AD:DP:GQ:PL	0/1:32,17:31:99:190,0,335
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+20	29436449	.	T	C	74.80	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=31.7694;MQ=60.00;MQ0=0;QD=1.92;SB=-22.52;VQSLOD=-2.4372;sumGLbyD=2.69	GT:AD:DP:GQ:PL	0/1:26,12:28:99:105,0,356
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+20	29440930	.	C	T	65.37	PASS	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=103.0543;MQ=60.00;MQ0=0;QD=0.46;SB=-25.04;VQSLOD=-2.4628;sumGLbyD=0.67	GT:AD:DP:GQ:PL	0/1:115,21:95:95.36:95,0,1503
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+20	29441057	.	C	T	45.77	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.11;HRun=2;HaplotypeScore=254.0858;MQ=60.00;MQ0=0;QD=0.45;SB=-17.68;VQSLOD=-2.8922;sumGLbyD=0.74	GT:AD:DP:GQ:PL	0/1:75,14:59:75.76:76,0,976
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+20	29467584	.	T	C	139.06	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=43.9104;MQ=60.00;MQ0=0;QD=3.39;SB=-32.45;VQSLOD=-1.6785;sumGLbyD=4.12	GT:AD:DP:GQ:PL	0/1:31,10:23:99:169,0,216
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+20	29468105	rs10871840	G	T	654.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=231;Dels=0.00;HRun=1;HaplotypeScore=183.8367;MQ=60.00;MQ0=0;QD=2.83;SB=-293.05;VQSLOD=-1.4589;sumGLbyD=2.96	GT:AD:DP:GQ:PL	0/1:155,74:162:99:684,0,1969
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+20	29468186	rs10871841	T	C	461.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.00;HRun=0;HaplotypeScore=155.1526;MQ=60.00;MQ0=0;QD=1.86;SB=-182.46;VQSLOD=-0.7522;sumGLbyD=1.98	GT:AD:DP:GQ:PL	0/1:187,54:167:99:492,0,2366
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+20	29468489	rs11152479	T	G	526.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=244;DS;Dels=0.06;HRun=0;HaplotypeScore=416.0168;MQ=60.00;MQ0=0;QD=2.16;SB=-132.38;VQSLOD=-1.1063;sumGLbyD=2.28	GT:AD:DP:GQ:PL	0/1:143,74:147:99:557,0,1955
+20	29468534	rs6087321	T	C	295.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=246;DS;Dels=0.15;HRun=1;HaplotypeScore=625.2170;MQ=60.00;MQ0=0;QD=1.20;SB=-124.62;VQSLOD=-1.6664;sumGLbyD=1.32	GT:AD:DP:GQ:PL	0/1:161,46:145:99:325,0,2142
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+20	52476951	.	T	A	206.06	PASS	AC=1;AF=0.50;AN=2;DP=164;DS;Dels=0.03;HRun=0;HaplotypeScore=194.9711;MQ=60.00;MQ0=0;QD=1.26;SB=-104.40;VQSLOD=-1.0620;sumGLbyD=1.44	GT:AD:DP:GQ:PL	0/1:111,41:112:99:236,0,1806
+20	52476958	.	C	T	153.11	PASS	AC=1;AF=0.50;AN=2;DP=164;DS;Dels=0.09;HRun=1;HaplotypeScore=294.3348;MQ=60.00;MQ0=0;QD=0.93;SB=-28.07;VQSLOD=-2.4629;sumGLbyD=1.12	GT:AD:DP:GQ:PL	0/1:114,28:98:99:183,0,1329
+20	52476975	.	C	T	291.85	PASS	AC=1;AF=0.50;AN=2;DP=155;DS;Dels=0.00;HRun=0;HaplotypeScore=182.7610;MQ=60.00;MQ0=0;QD=1.88;SB=-56.75;VQSLOD=-0.9911;sumGLbyD=2.08	GT:AD:DP:GQ:PL	0/1:107,37:93:99:322,0,1071
+20	52476992	.	T	C	399.94	PASS	AC=1;AF=0.50;AN=2;DP=150;DS;Dels=0.02;HRun=0;HaplotypeScore=167.8167;MQ=60.00;MQ0=0;QD=2.67;SB=-117.76;VQSLOD=-0.4013;sumGLbyD=2.87	GT:AD:DP:GQ:PL	0/1:97,47:113:99:430,0,1463
+20	52477015	.	G	A	109.08	PASS	AC=1;AF=0.50;AN=2;DP=143;DS;Dels=0.06;HRun=1;HaplotypeScore=273.2263;MQ=60.00;MQ0=0;QD=0.76;SB=-7.20;VQSLOD=-2.6386;sumGLbyD=0.97	GT:AD:DP:GQ:PL	0/1:96,38:91:99:139,0,1203
+20	52477026	.	A	T	292.55	PASS	AC=1;AF=0.50;AN=2;DP=144;DS;Dels=0.05;HRun=2;HaplotypeScore=225.5374;MQ=60.00;MQ0=0;QD=2.03;SB=-47.13;VQSLOD=-2.1255;sumGLbyD=2.24	GT:AD:DP:GQ:PL	0/1:92,39:92:99:323,0,1293
+20	52477058	.	G	A	562.78	PASS	AC=1;AF=0.50;AN=2;DP=136;DS;Dels=0.02;HRun=0;HaplotypeScore=142.1341;MQ=60.00;MQ0=0;QD=4.14;SB=-204.35;VQSLOD=-0.2761;sumGLbyD=4.36	GT:AD:DP:GQ:PL	0/1:88,44:106:99:593,0,1304
+20	52477066	.	T	C	173.83	PASS	AC=1;AF=0.50;AN=2;DP=137;DS;Dels=0.00;HRun=0;HaplotypeScore=82.8043;MQ=60.00;MQ0=0;QD=1.27;SB=-66.19;VQSLOD=-1.9920;sumGLbyD=1.49	GT:AD:DP:GQ:PL	0/1:104,30:90:99:204,0,1317
+20	52477120	.	G	T	364.17	PASS	AC=1;AF=0.50;AN=2;DP=128;DS;Dels=0.03;HRun=0;HaplotypeScore=111.3768;MQ=60.00;MQ0=0;QD=2.85;SB=-43.39;VQSLOD=-1.0840;sumGLbyD=3.08	GT:AD:DP:GQ:PL	0/1:86,36:88:99:394,0,1159
+20	52477162	.	A	G	231.10	PASS	AC=1;AF=0.50;AN=2;DP=122;DS;Dels=0.11;HRun=1;HaplotypeScore=301.7020;MQ=60.00;MQ0=0;QD=1.89;SB=-111.39;VQSLOD=-1.5861;sumGLbyD=2.14	GT:AD:DP:GQ:PL	0/1:77,28:72:99:261,0,972
+20	52477216	rs56158048	C	G	120.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=107;DS;Dels=0.03;HRun=0;HaplotypeScore=206.1839;MQ=60.00;MQ0=0;QD=1.13;SB=-38.53;VQSLOD=-1.3969;sumGLbyD=1.41	GT:AD:DP:GQ:PL	0/1:74,27:61:99:151,0,926
+20	52477243	.	G	A	129.98	PASS	AC=1;AF=0.50;AN=2;DP=105;DS;Dels=0.07;HRun=1;HaplotypeScore=182.7841;MQ=60.00;MQ0=0;QD=1.24;SB=-58.90;VQSLOD=-2.0782;sumGLbyD=1.52	GT:AD:DP:GQ:PL	0/1:72,24:55:99:160,0,805
+20	52477258	.	C	T	133.06	PASS	AC=1;AF=0.50;AN=2;DP=102;DS;Dels=0.07;HRun=1;HaplotypeScore=145.0557;MQ=60.00;MQ0=0;QD=1.30;SB=-61.24;VQSLOD=-2.1698;sumGLbyD=1.60	GT:AD:DP:GQ:PL	0/1:59,35:56:99:163,0,791
+20	52477282	.	G	A	56.71	PASS	AC=1;AF=0.50;AN=2;DP=94;DS;Dels=0.18;HRun=0;HaplotypeScore=332.8721;MQ=60.00;MQ0=0;QD=0.60;SB=-29.83;VQSLOD=-1.8082;sumGLbyD=0.92	GT:AD:DP:GQ:PL	0/1:47,26:40:86.70:87,0,470
+20	52477289	.	C	T	105	PASS	AC=1;AF=0.50;AN=2;DP=93;DS;Dels=0.15;HRun=1;HaplotypeScore=235.1778;MQ=60.00;MQ0=0;QD=1.13;SB=-49.61;VQSLOD=-2.1302;sumGLbyD=1.45	GT:AD:DP:GQ:PL	0/1:51,25:42:99:135,0,587
+20	56523601	rs6025925	G	C	148.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.03;HRun=0;HaplotypeScore=30.0349;MQ=60.00;MQ0=0;QD=4.65;SB=-87.54;VQSLOD=-1.5376;sumGLbyD=5.58	GT:AD:DP:GQ:PL	0/1:18,13:27:99:179,0,300
+20	56523643	rs6025926	T	C	134.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=53.9853;MQ=60.00;MQ0=0;QD=3.13;SB=-35.08;VQSLOD=-1.5668;sumGLbyD=3.83	GT:AD:DP:GQ:PL	0/1:26,15:30:99:165,0,339
+20	56523799	rs6025927	T	C	155.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.04;HRun=0;HaplotypeScore=77.7376;MQ=60.00;MQ0=0;QD=2.99;SB=-47.18;VQSLOD=-1.2535;sumGLbyD=3.57	GT:AD:DP:GQ:PL	0/1:26,22:31:99:185,0,361
+20	56524660	rs59556206	C	T	33.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=38.6534;MQ=60.00;MQ0=0;QD=1.21;SB=-26.41;VQSLOD=-2.8205;sumGLbyD=2.28	GT:AD:DP:GQ:PL	0/1:14,14:11:63.81:64,0,136
+20	57577935	rs163798	A	G	178.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.08;HRun=0;HaplotypeScore=74.4582;MQ=60.00;MQ0=0;QD=4.45;SB=-103.21;VQSLOD=-1.0021;sumGLbyD=5.20	GT:AD:DP:GQ:PL	0/1:20,14:33:99:208,0,387
+20	57578420	rs56352943	A	G	552.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=141.5473;MQ=60.00;MQ0=0;QD=4.50;SB=-253.33;VQSLOD=-0.4388;sumGLbyD=4.74	GT:AD:DP:GQ:PL	0/1:79,42:96:99:583,0,1028
+20	57578508	rs163800	T	C	1342.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=122;Dels=0.04;HRun=0;HaplotypeScore=143.0812;MQ=60.00;MQ0=0;QD=11.00;SB=-641.51;VQSLOD=-1.6803;sumGLbyD=11.27	GT:AD:DP:GQ:PL	1/1:4,102:73:99:1375,207,0
+20	57578614	rs163801	A	G	1331.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=127;Dels=0.20;HRun=1;HaplotypeScore=423.7909;MQ=60.00;MQ0=0;QD=10.48;SB=-576.57;VQSLOD=-1.9233;sumGLbyD=10.74	GT:AD:DP:GQ:PL	1/1:7,88:77:99:1364,134,0
+20	57578852	rs163802	C	G	76.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=137;Dels=0.32;HRun=3;HaplotypeScore=664.1589;MQ=60.00;MQ0=0;QD=0.56;SB=1.54;VQSLOD=-5.5650;sumGLbyD=0.78	GT:AD:DP:GQ:PL	0/1:70,20:69:99:107,0,827
+20	58170882	rs2180680	G	A	590.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.03;HRun=0;HaplotypeScore=118.1657;MQ=60.00;MQ0=0;QD=4.96;SB=-247.23;VQSLOD=-0.6701;sumGLbyD=5.21	GT:AD:DP:GQ:PL	0/1:64,49:97:99:620,0,890
+20	58170900	rs4812116	T	C	481.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.02;HRun=0;HaplotypeScore=188.7468;MQ=60.00;MQ0=0;QD=3.85;SB=-152.37;VQSLOD=-0.3499;sumGLbyD=4.09	GT:AD:DP:GQ:PL	0/1:76,40:92:99:511,0,1002
+20	59455378	rs2016776	A	G	65.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=13.5277;MQ=60.00;MQ0=0;QD=3.27;SB=-31.46;VQSLOD=-2.0555;sumGLbyD=4.77	GT:AD:DP:GQ:PL	0/1:12,8:15:95.35:95,0,154
+20	59456370	rs6027899	T	C	125.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.03;HRun=0;HaplotypeScore=34.9707;MQ=60.00;MQ0=0;QD=3.68;SB=-58.07;VQSLOD=-1.5221;sumGLbyD=4.57	GT:AD:DP:GQ:PL	0/1:15,16:23:99:155,0,223
+20	59456392	rs6027900	A	G	156.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.03;HRun=0;HaplotypeScore=33.6051;MQ=60.00;MQ0=0;QD=4.88;SB=-70.80;VQSLOD=-1.7700;sumGLbyD=5.81	GT:AD:DP:GQ:PL	0/1:19,12:19:99:186,0,148
+20	59456420	rs2426932	T	C	153.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.11;HRun=1;HaplotypeScore=71.3263;MQ=60.00;MQ0=0;QD=5.49;SB=-80.48;VQSLOD=-2.1741;sumGLbyD=6.57	GT:AD:DP:GQ:PL	0/1:11,12:13:13.64:184,0,14
+20	59456449	rs2426933	C	A	46.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=23.7046;MQ=60.00;MQ0=0;QD=1.72;SB=-8.75;VQSLOD=-3.4501;sumGLbyD=2.83	GT:AD:DP:GQ:PL	0/1:19,8:14:76.53:77,0,171
+20	60509879	rs4925318	A	G	160.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.05;HRun=0;HaplotypeScore=142.3092;MQ=60.00;MQ0=0;QD=2.05;SB=-83.96;VQSLOD=-0.8706;sumGLbyD=2.44	GT:AD:DP:GQ:PL	0/1:46,27:50:99:190,0,597
+20	60509955	rs4925319	G	A	342.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.01;HRun=0;HaplotypeScore=106.2051;MQ=60.00;MQ0=0;QD=4.03;SB=-121.59;VQSLOD=-0.5877;sumGLbyD=4.39	GT:AD:DP:GQ:PL	0/1:44,36:63:99:373,0,723
+20	60509995	rs4925320	C	A	279.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.04;HRun=2;HaplotypeScore=135.2499;MQ=60.00;MQ0=0;QD=3.01;SB=-127.49;VQSLOD=-2.0055;sumGLbyD=3.33	GT:AD:DP:GQ:PL	0/1:50,36:60:99:310,0,707
+20	60510043	rs4925321	G	A	384.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.03;HRun=0;HaplotypeScore=124.2625;MQ=60.00;MQ0=0;QD=3.81;SB=-186.91;VQSLOD=-0.2629;sumGLbyD=4.11	GT:AD:DP:GQ:PL	0/1:56,34:73:99:415,0,685
+20	60510337	rs2153936	C	T	628.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=214;Dels=0.02;HRun=0;HaplotypeScore=247.2870;MQ=60.00;MQ0=0;QD=2.94;SB=-212.89;VQSLOD=-0.3082;sumGLbyD=3.08	GT:AD:DP:GQ:PL	0/1:123,73:152:99:658,0,1869
+20	60510417	rs6089559	C	T	778.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.00;HRun=0;HaplotypeScore=244.9003;MQ=60.00;MQ0=0;QD=3.33;SB=-386.26;VQSLOD=-0.5199;sumGLbyD=3.45	GT:AD:DP:GQ:PL	0/1:143,81:135:99:808,0,1482
+20	60510422	rs2153935	A	C	620.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.12;HRun=1;HaplotypeScore=607.6288;MQ=60.00;MQ0=0;QD=2.65;SB=-246.28;VQSLOD=-1.4133;sumGLbyD=2.78	GT:AD:DP:GQ:PL	0/1:133,62:163:99:651,0,1992
+20	60510750	rs6142885	A	C	2258.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=190;Dels=0.09;HRun=1;HaplotypeScore=359.1129;MQ=60.00;MQ0=0;QD=11.89;SB=-1072.04;VQSLOD=-5.5742;sumGLbyD=12.06	GT:AD:DP:GQ:PL	1/1:8,150:108:99:2291,269,0
+20	61816492	rs6090278	C	T	224.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.06;HRun=0;HaplotypeScore=79.7334;MQ=60.00;MQ0=0;QD=4.39;SB=-91.32;VQSLOD=-1.0462;sumGLbyD=4.98	GT:AD:DP:GQ:PL	0/1:24,21:36:99:254,0,327
+20	61816789	rs6090279	G	A	652.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.05;HRun=0;HaplotypeScore=225.7796;MQ=60.00;MQ0=0;QD=4.10;SB=-320.92;VQSLOD=-0.4184;sumGLbyD=4.29	GT:AD:DP:GQ:PL	0/1:91,57:114:99:682,0,1042
+20	61816951	rs6090280	T	C	866.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;Dels=0.06;HRun=0;HaplotypeScore=350.3056;MQ=60.00;MQ0=0;QD=4.09;SB=-225.82;VQSLOD=-1.2257;sumGLbyD=4.23	GT:AD:DP:GQ:PL	0/1:106,84:147:99:897,0,1528
+20	61817385	rs6089856	C	T	895.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=170;Dels=0.04;HRun=0;HaplotypeScore=200.4081;MQ=60.00;MQ0=0;QD=5.27;SB=-440.80;VQSLOD=-1.1392;sumGLbyD=5.44	GT:AD:DP:GQ:PL	0/1:81,73:123:99:926,0,954
+20	61817589	rs6090281	C	T	390.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.01;HRun=0;HaplotypeScore=87.2202;MQ=60.00;MQ0=0;QD=3.83;SB=-141.97;VQSLOD=-0.5485;sumGLbyD=4.12	GT:AD:DP:GQ:PL	0/1:59,42:63:99:421,0,602
+20	61967037	rs9680065	G	A	233.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.08;HRun=1;HaplotypeScore=199.3982;MQ=60.00;MQ0=0;QD=2.18;SB=-129.21;VQSLOD=-1.4181;sumGLbyD=2.46	GT:AD:DP:GQ:PL	0/1:59,37:53:99:263,0,607
+20	61967440	rs6011759	C	G	133.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=86.7767;MQ=60.00;MQ0=0;QD=4.16;SB=-74.81;VQSLOD=-0.6803;sumGLbyD=5.19	GT:AD:DP:GQ:PL	1/1:8,23:8:23.74:166,24,0
+20	62388627	rs6089973	C	T	150.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.07;HRun=1;HaplotypeScore=41.2425;MQ=60.00;MQ0=0;QD=5.37;SB=-53.10;VQSLOD=-2.9388;sumGLbyD=6.44	GT:AD:DP:GQ:PL	0/1:14,11:20:99:180,0,120
+20	62388655	rs6011086	C	T	272.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.32;HRun=4;HaplotypeScore=103.6966;MQ=60.00;MQ0=0;QD=8.80;SB=-71.11;VQSLOD=-12.9297;sumGLbyD=9.87	GT:AD:DP:GQ:PL	1/1:2,17:15:21.18:306,21,0
+20	62388897	rs6010640	T	C	426.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.13;HRun=0;HaplotypeScore=142.0259;MQ=60.00;MQ0=0;QD=7.76;SB=-188.69;VQSLOD=-0.8076;sumGLbyD=8.36	GT:AD:DP:GQ:PL	1/1:8,36:28:34.67:460,35,0

public/testdata/VariantEval/silent.txt

@@ -0,0 +1 @@
+20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0

public/testdata/VariantEval/transition.vcf

@@ -0,0 +1,3 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0

public/testdata/VariantEval/transversion.vcf

@@ -0,0 +1,3 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
+20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0

public/testdata/allelesForUG.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
+20	10000688	.	C	G	213.10	.	AC=1;AF=0.25;AN=4;DP=46;Dels=0.00;HRun=1;HaplotypeScore=4.8419;MQ=94.33;MQ0=0;QD=8.20;SB=-139.26;sumGLbyD=9.47	GT:AD:DP:GQ:PL	0/1:15,10:23:99:246,0,364	0/0:20,0:20:60.12:0,60,635
+20	10001023	.	T	A	291.78	.	AC=1;AF=0.25;AN=4;DP=70;Dels=0.00;HRun=0;HaplotypeScore=8.1219;MQ=90.98;MQ0=0;QD=10.81;SB=-108.18;sumGLbyD=12.03	GT:AD:DP:GQ:PL	0/0:42,0:35:99:0,102,1144	0/1:13,14:24:99:325,0,283
+20	10001267	.	G	A	202.35	.	AC=1;AF=0.25;AN=4;DP=69;Dels=0.00;HRun=0;HaplotypeScore=8.5086;MQ=88.37;MQ0=0;QD=6.98;SB=-92.88;sumGLbyD=8.12	GT:AD:DP:GQ:PL	0/0:40,0:31:93.20:0,93,983	0/1:17,12:25:99:235,0,371
+20	10001395	.	G	A	1022.27	.	AC=2;AF=0.50;AN=4;DP=82;Dels=0.00;HRun=0;HaplotypeScore=8.3689;MQ=90.24;MQ0=0;QD=23.77;SB=-409.81;sumGLbyD=24.72	GT:AD:DP:GQ:PL	0/0:35,0:29:87.23:0,87,972	1/1:0,43:36:99:1063,108,0

public/testdata/amplicon_interval_table1.table

@@ -0,0 +1,6 @@
+HEADERpos	name
+20:207334-207494	20_207414
+20:792042-792202	20_792122
+20:994065-994225	20_994145
+20:1074150-1074310	20_1074230
+20:1084250-1084410	20_1084330

public/testdata/amplicon_mask_sites.vcf

@@ -0,0 +1,11 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
+20	207414	.	G	A	77.12	PASS	.	GT	0/0
+20	207416	.	A	AGGC	49422.34	PASS	.	GT	0/0
+20	792076	.	A	G	2637.15	HaplotypeScore	.	GT	0/0
+20	792080	.	T	G	161.83	PASS	.	GT	0/0
+20	792087	.	CGGT	C	179.84	ReadPosRankSum	.	GT	0/0
+20	792106	.	C	G	32.59	PASS	.	GT	0/0
+20	792140	.	C	G	409.75	PASS	.	GT	0/0
+20	1084319	.	T	A,C	22.24	PASS	.	GT	0/0
+20	1084348	.	TACCACCCCACACA	T	482.84	PASS	.	GT	0/0

public/testdata/badIntervalLocations.list

@@ -0,0 +1,2 @@
+chr1:10-7
+chr1:1-5

public/testdata/combine.1.vcf

@@ -0,0 +1,10 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FILTER=<ID=FAIL,Description="Fail">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891
+20	9999996	.	A	ACT	.	PASS	.	GT:GQ	0/1:30
+20	10000000	.	T	G	.	PASS	.	GT:GQ	0/1:30
+20	10000117	.	C	T	.	FAIL	.	GT:GQ	0/1:30
+20	10000211	.	C	T	.	PASS	.	GT:GQ	0/1:30
+20	10001436	.	A	AGG	.	PASS	.	GT:GQ	1/1:30

public/testdata/combine.2.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	9999996	.	A	ACT	.	PASS	.	GT:GQ	0/1:30
+20	10000117	.	C	T	.	FAIL	.	GT:GQ	0/1:30
+20	10000211	.	C	T	.	FAIL	.	GT:GQ	0/1:30
+20	10000598	.	T	A	.	PASS	.	GT:GQ	1/1:30
+20	10001436	.	A	AGGCT	.	PASS	.	GT:GQ	1/1:30

public/testdata/combine.3.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
+20	10000000	.	T	G	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
+20	10000117	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	0/0:0,10,80
+20	10000211	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	1/1:90,10,0

public/testdata/combine.4.vcf

@@ -0,0 +1,5 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12893	NA12894
+20	10000000	.	T	A	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
+20	10000117	.	C	T	.	PASS	.	GT	0/1	0/0
+20	10000211	.	C	A	.	PASS	.	GT:PL	0/1:10,0,10	./.

public/testdata/combine.5.vcf

@@ -0,0 +1,5 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
+20	10000000	.	T	G	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
+20	10000117	.	C	A,T	.	PASS	.	GT:PL	0/1:10,0,10	0/2:0,10,80
+20	10000211	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	1/1:90,10,0

public/testdata/combine.6.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
+20	10000000	.	T	G	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
+20	10000117	.	C	A,T	.	PASS	.	GT:PL	0/1:10,0,10	0/2:0,10,80
+20	10000211	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	1/1:90,10,0
+20	10001436	.	A	AGG,T	.	PASS	.	GT:GQ	1/1:30
+

public/testdata/complexExample1.vcf

@@ -0,0 +1,30 @@
+##fileformat=VCFv4.0
+##source=ArbitrarySource
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=AlleleBalance,Number=1,Type=Float,Description="Allele balance (old name)">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples">
+##INFO=<ID=OnOffGenotype,Number=1,Type=Float,Description="???">
+##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="Number of spanning deletions">
+##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS mapping quality (old name)">
+##INFO=<ID=FisherStrand,Number=1,Type=Float,Description="Fisher strand (old name)">
+##INFO=<ID=DoC,Number=1,Type=Integer,Description="DP (old name)">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##reference=human_b36_both.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
+1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
+1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
+1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
+1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
+1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
+1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
+1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
+1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
+1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/complexExample2.vcf

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##source=ArbitrarySource
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##reference=human_b36_both.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
+1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
+1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
+1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
+1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
+1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
+1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
+1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
+1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
+1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/complexExample3.vcf

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##source=ArbitrarySource
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##reference=human_b36_both.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
+1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
+1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
+1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
+1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
+1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
+1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
+1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
+1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
+1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/exampleFASTA-3contigs.fasta

@@ -0,0 +1,24 @@
+>chr1
+AAAAA
+AAAAA
+AAAAA
+AA
+
+
+>chr2
+BBBBBBB
+BBBBBBB
+BBBBBBB
+
+>chr3
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+CCCCCCCCCC
+

public/testdata/exampleFASTA-windows.fasta

@@ -0,0 +1,7 @@
+>chr2
+AAAAAAA
+AAAAAAA
+DDDDDDD
+CCCCCCC
+D
+

public/testdata/exampleGATKReport.eval

@@ -0,0 +1,36 @@
+##:GATKReport.v0.1 CompOverlap : The overlap between eval and comp sites
+CompOverlap  CompRod  EvalRod  JexlExpression  Novelty  nEvalVariants  nCompVariants  novelSites  nVariantsAtComp  compRate  nConcordant  concordantRate
+CompOverlap  none     eval     none            all      0              0              0           0                0.00000000  0            0.00000000    
+CompOverlap  none     eval     none            known    0              0              0           0                0.00000000  0            0.00000000    
+CompOverlap  none     eval     none            novel    0              0              0           0                0.00000000  0            0.00000000    
+
+##:GATKReport.v0.1 CountVariants : Counts different classes of variants in the sample
+CountVariants  CompRod  EvalRod  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate  variantRatePerBp  nSNPs  nMNPs  nInsertions  nDeletions  nComplex  nNoCalls  nHets  nHomRef  nHomVar  nSingletons  heterozygosity  heterozygosityPerBp  hetHomRatio  indelRate  indelRatePerBp  deletionInsertionRatio
+CountVariants  none     eval     none            all      100000          100000       100000    0             0.00000000   0.00000000        0      0      0            0           0         99872     0      128      0        0            0.00000000      0.00000000           0.00000000   0.00000000  0.00000000      0.00000000            
+CountVariants  none     eval     none            known    100000          0            0         0             0.00000000   0.00000000        0      0      0            0           0         0         0      0        0        0            0.00000000      0.00000000           0.00000000   0.00000000  0.00000000      0.00000000            
+CountVariants  none     eval     none            novel    100000          100000       100000    0             0.00000000   0.00000000        0      0      0            0           0         99872     0      128      0        0            0.00000000      0.00000000           0.00000000   0.00000000  0.00000000      0.00000000            
+
+##:GATKReport.v0.1 SimpleMetricsByAC.metrics : TiTv by allele count
+SimpleMetricsByAC.metrics  CompRod  EvalRod  JexlExpression  Novelty  row  AC  nTi  nTv  n  TiTv
+SimpleMetricsByAC.metrics  none     eval     none            all      ac0  0   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            all      ac1  1   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            all      ac2  2   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            known    ac0  0   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            known    ac1  1   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            known    ac2  2   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            novel    ac0  0   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            novel    ac1  1   0    0    0  0.0 
+SimpleMetricsByAC.metrics  none     eval     none            novel    ac2  2   0    0    0  0.0 
+
+##:GATKReport.v0.1 TiTvVariantEvaluator : Ti/Tv Variant Evaluator
+TiTvVariantEvaluator  CompRod  EvalRod  JexlExpression  Novelty  nTi  nTv  tiTvRatio  nTiInComp  nTvInComp  TiTvRatioStandard
+TiTvVariantEvaluator  none     eval     none            all      0    0    0.00000000  0          0          0.00000000       
+TiTvVariantEvaluator  none     eval     none            known    0    0    0.00000000  0          0          0.00000000       
+TiTvVariantEvaluator  none     eval     none            novel    0    0    0.00000000  0          0          0.00000000       
+
+##:GATKReport.v0.1 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay
+ValidationReport  CompRod  EvalRod  JexlExpression  Novelty  nComp  TP  FP  FN  TN  sensitivity  PPV  FDR  CompMonoEvalNoCall  CompMonoEvalFiltered  CompMonoEvalMono  CompMonoEvalPoly  CompPolyEvalNoCall  CompPolyEvalFiltered  CompPolyEvalMono  CompPolyEvalPoly  CompFiltered  nDifferentAlleleSites
+ValidationReport  none     eval     none            all      0      0   0   0   0   NaN          NaN  NaN  0                   0                     0                 0                 0                   0                     0                 0                 0             0                    
+ValidationReport  none     eval     none            known    0      0   0   0   0   NaN          NaN  NaN  0                   0                     0                 0                 0                   0                     0                 0                 0             0                    
+ValidationReport  none     eval     none            novel    0      0   0   0   0   NaN          NaN  NaN  0                   0                     0                 0                 0                   0                     0                 0                 0             0                    
+

public/testdata/exampleGATKReportv1.tbl

@@ -0,0 +1,36 @@
+#:GATKReport.v1.0:5
+#:GATKTable:false:11:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%.2f
+#:GATKTable:CompOverlap:The overlap between eval and comp sites
+CompOverlap  CompRod  EvalRod  JexlExpression  Novelty  nEvalVariants  novelSites  nVariantsAtComp  compRate  nConcordant  concordantRate
+CompOverlap  dbsnp    eval     none            all                481          12              469     97.51          468           99.79
+CompOverlap  dbsnp    eval     none            known              469           0              469    100.00          468           99.79
+CompOverlap  dbsnp    eval     none            novel               12          12                0      0.00            0            0.00
+
+#:GATKTable:false:30:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f
+#:GATKTable:CountVariants:Counts different classes of variants in the sample
+CountVariants  CompRod  EvalRod  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate            variantRatePerBp  nSNPs  nMNPs  nInsertions  nDeletions  nComplex  nSymbolic  nMixed  nNoCalls  nHets  nHomRef  nHomVar  nSingletons  nHomDerived  heterozygosity  heterozygosityPerBp  hetHomRatio  indelRate  indelRatePerBp  deletionInsertionRatio
+CountVariants  dbsnp    eval     none            all            63025520          481         0           481    7.63182913841885E-6          131030.0    481      0            0           0         0          0       0         0    298        0      183          298            0        4.73e-06            211495.00         1.63   0.00e+00            0.00                    0.00
+CountVariants  dbsnp    eval     none            known          63025520          469         0           469   7.441430074674513E-6          134382.0    469      0            0           0         0          0       0         0    288        0      181          288            0        4.57e-06            218838.00         1.59   0.00e+00            0.00                    0.00
+CountVariants  dbsnp    eval     none            novel          63025520           12         0            12  1.9039906374433722E-7         5252126.0     12      0            0           0         0          0       0         0     10        0        2           10            0        1.59e-07           6302552.00         5.00   0.00e+00            0.00                    0.00
+
+#:GATKTable:false:14:3:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%s:%s:%.2f
+#:GATKTable:TiTvVariantEvaluator:Ti/Tv Variant Evaluator
+TiTvVariantEvaluator  CompRod  EvalRod  JexlExpression  Novelty  nTi  nTv  tiTvRatio  nTiInComp  nTvInComp  TiTvRatioStandard  nTiDerived  nTvDerived  tiTvDerivedRatio
+TiTvVariantEvaluator  dbsnp    eval     none            all      382   99       3.86     203506      85497               2.38           0           0              0.00
+TiTvVariantEvaluator  dbsnp    eval     none            known    374   95       3.94        360         91               3.96           0           0              0.00
+TiTvVariantEvaluator  dbsnp    eval     none            novel      8    4       2.00     203146      85406               2.38           0           0              0.00
+
+#:GATKTable:false:24:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%.2f:%.2f:%.2f:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s
+#:GATKTable:ValidationReport:Assess site accuracy and sensitivity of callset against follow-up validation assay
+ValidationReport  CompRod  EvalRod  JexlExpression  Novelty  nComp   TP   FP  FN      TN  sensitivity  specificity  PPV     FDR   CompMonoEvalNoCall  CompMonoEvalFiltered  CompMonoEvalMono  CompMonoEvalPoly  CompPolyEvalNoCall  CompPolyEvalFiltered  CompPolyEvalMono  CompPolyEvalPoly  CompFiltered  nDifferentAlleleSites
+ValidationReport  dbsnp    eval     none            all      369102  469   0  368633   0         0.13       100.00  100.00  0.00                   0                     0                 0                 0              368633                     0                 0               469             0                      0
+ValidationReport  dbsnp    eval     none            known       469  469   0       0   0       100.00       100.00  100.00  0.00                   0                     0                 0                 0                   0                     0                 0               469             0                      0
+ValidationReport  dbsnp    eval     none            novel    368633    0   0  368633   0         0.00       100.00     NaN   NaN                   0                     0                 0                 0              368633                     0                 0                 0             0                      0
+
+#:GATKTable:false:20:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%.1f:%s:%s:%s:%.1f:%s:%s:%s
+#:GATKTable:VariantSummary:1000 Genomes Phase I summary of variants table
+VariantSummary  CompRod  EvalRod  JexlExpression  Novelty  nSamples  nProcessedLoci  nSNPs  TiTvRatio  SNPNoveltyRate  nSNPsPerSample  TiTvRatioPerSample  SNPDPPerSample  nIndels  IndelNoveltyRate  nIndelsPerSample  IndelDPPerSample  nSVs  SVNoveltyRate  nSVsPerSample
+VariantSummary  dbsnp    eval     none            all             1        63025520    481       3.86            0.02             481                3.86           481.0        0                NA                 0               0.0     0             NA              0
+VariantSummary  dbsnp    eval     none            known           1        63025520    469       3.94            0.00             469                3.94           469.0        0                NA                 0               0.0     0             NA              0
+VariantSummary  dbsnp    eval     none            novel           1        63025520     12       2.00            1.00              12                2.00            12.0        0                NA                 0               0.0     0             NA              0
+

public/testdata/exampleGATKReportv2.tbl

@@ -0,0 +1,36 @@
+#:GATKReport.v1.1:5
+#:GATKTable:11:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%.2f
+#:GATKTable:CompOverlap:The overlap between eval and comp sites
+CompOverlap  CompRod  EvalRod  JexlExpression  Novelty  nEvalVariants  novelSites  nVariantsAtComp  compRate  nConcordant  concordantRate
+CompOverlap  dbsnp    eval     none            all                481          12              469     97.51          468           99.79
+CompOverlap  dbsnp    eval     none            known              469           0              469    100.00          468           99.79
+CompOverlap  dbsnp    eval     none            novel               12          12                0      0.00            0            0.00
+
+#:GATKTable:30:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f
+#:GATKTable:CountVariants:Counts different classes of variants in the sample
+CountVariants  CompRod  EvalRod  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate            variantRatePerBp  nSNPs  nMNPs  nInsertions  nDeletions  nComplex  nSymbolic  nMixed  nNoCalls  nHets  nHomRef  nHomVar  nSingletons  nHomDerived  heterozygosity  heterozygosityPerBp  hetHomRatio  indelRate  indelRatePerBp  deletionInsertionRatio
+CountVariants  dbsnp    eval     none            all            63025520          481         0           481    7.63182913841885E-6          131030.0    481      0            0           0         0          0       0         0    298        0      183          298            0        4.73e-06            211495.00         1.63   0.00e+00            0.00                    0.00
+CountVariants  dbsnp    eval     none            known          63025520          469         0           469   7.441430074674513E-6          134382.0    469      0            0           0         0          0       0         0    288        0      181          288            0        4.57e-06            218838.00         1.59   0.00e+00            0.00                    0.00
+CountVariants  dbsnp    eval     none            novel          63025520           12         0            12  1.9039906374433722E-7         5252126.0     12      0            0           0         0          0       0         0     10        0        2           10            0        1.59e-07           6302552.00         5.00   0.00e+00            0.00                    0.00
+
+#:GATKTable:14:3:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%s:%s:%.2f
+#:GATKTable:TiTvVariantEvaluator:Ti/Tv Variant Evaluator
+TiTvVariantEvaluator  CompRod  EvalRod  JexlExpression  Novelty  nTi  nTv  tiTvRatio  nTiInComp  nTvInComp  TiTvRatioStandard  nTiDerived  nTvDerived  tiTvDerivedRatio
+TiTvVariantEvaluator  dbsnp    eval     none            all      382   99       3.86     203506      85497               2.38           0           0              0.00
+TiTvVariantEvaluator  dbsnp    eval     none            known    374   95       3.94        360         91               3.96           0           0              0.00
+TiTvVariantEvaluator  dbsnp    eval     none            novel      8    4       2.00     203146      85406               2.38           0           0              0.00
+
+#:GATKTable:24:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%.2f:%.2f:%.2f:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s
+#:GATKTable:ValidationReport:Assess site accuracy and sensitivity of callset against follow-up validation assay
+ValidationReport  CompRod  EvalRod  JexlExpression  Novelty  nComp   TP   FP  FN      TN  sensitivity  specificity  PPV     FDR   CompMonoEvalNoCall  CompMonoEvalFiltered  CompMonoEvalMono  CompMonoEvalPoly  CompPolyEvalNoCall  CompPolyEvalFiltered  CompPolyEvalMono  CompPolyEvalPoly  CompFiltered  nDifferentAlleleSites
+ValidationReport  dbsnp    eval     none            all      369102  469   0  368633   0         0.13       100.00  100.00  0.00                   0                     0                 0                 0              368633                     0                 0               469             0                      0
+ValidationReport  dbsnp    eval     none            known       469  469   0       0   0       100.00       100.00  100.00  0.00                   0                     0                 0                 0                   0                     0                 0               469             0                      0
+ValidationReport  dbsnp    eval     none            novel    368633    0   0  368633   0         0.00       100.00     NaN   NaN                   0                     0                 0                 0              368633                     0                 0                 0             0                      0
+
+#:GATKTable:20:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%.1f:%s:%s:%s:%.1f:%s:%s:%s
+#:GATKTable:VariantSummary:1000 Genomes Phase I summary of variants table
+VariantSummary  CompRod  EvalRod  JexlExpression  Novelty  nSamples  nProcessedLoci  nSNPs  TiTvRatio  SNPNoveltyRate  nSNPsPerSample  TiTvRatioPerSample  SNPDPPerSample  nIndels  IndelNoveltyRate  nIndelsPerSample  IndelDPPerSample  nSVs  SVNoveltyRate  nSVsPerSample
+VariantSummary  dbsnp    eval     none            all             1        63025520    481       3.86            0.02             481                3.86           481.0        0                NA                 0               0.0     0             NA              0
+VariantSummary  dbsnp    eval     none            known           1        63025520    469       3.94            0.00             469                3.94           469.0        0                NA                 0               0.0     0             NA              0
+VariantSummary  dbsnp    eval     none            novel           1        63025520     12       2.00            1.00              12                2.00            12.0        0                NA                 0               0.0     0             NA              0
+

public/testdata/fakeHM3.vcf

@@ -0,0 +1,9 @@
+##fileformat=VCFv4.0
+##INFO=<ID=XX,Number=0,Type=Flag,Description="XX Membership">
+##FOO
+##BAR
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
+1	10001292	.	G	A	.	PASS	.	GT	1/0
+1	10006296	.	C	T	.	PASS	.	GT	0/1
+1	10042312	.	G	C	.	FAIL	.	GT	1/0
+1	10048142	.	A	G	.	PASS	.	GT	1/1

public/testdata/forLeftAlignVariantsTest.vcf

@@ -0,0 +1,5 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	194723643	rs67631353	CA	CCC	.	.	.
+2	179391647	.	T	TT	.	.	.
+20	120123	rs34533099	A	AGA	.	.	.

public/testdata/header.txt

@@ -0,0 +1,14 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
+##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
+##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
+##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
+##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625

public/testdata/indbnp129_notindbsnp132.txt

@@ -0,0 +1 @@
+20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37

public/testdata/indbnp132_notindbsnp129.txt

@@ -0,0 +1,2 @@
+20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
+20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.

public/testdata/indelAllelesForUG.vcf

@@ -0,0 +1,43 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=[20:10,000,000-10,100,000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_b36_both.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false genotype_likelihoods_model=DINDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 insertionStartProbability=0.0010 insertionEndProbability=0.5 alphaDeletionProbability=0.0010 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=40.0 indelHaplotypeSize=80 indelDebug=true s1=null s2=null dovit=false newlike=false exactCalculation=LINEAR_EXPERIMENTAL output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub verbose_mode=null metrics_file=null annotation=[]"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
+20	10015049	.	TAAAAAAA	T	388.73	.	AC=3;AF=0.75;AN=4;DP=47;Dels=0.15;HRun=25;HaplotypeScore=18.5023;MQ=76.79;MQ0=9;QD=8.27;SB=-216.09;sumGLbyD=9.26	GT:AD:DP:GQ:PL	1/1:20,5:10:14.03:205,14,0	0/1:20,0:19:99:230,0,202
+20	10018938	.	G	GA	943.48	.	AC=3;AF=0.75;AN=4;DP=56;Dels=0.00;HRun=1;HaplotypeScore=8.3072;MQ=98.07;MQ0=0;QD=16.85;SB=-456.74;sumGLbyD=17.68	GT:AD:DP:GQ:PL	1/1:3,23:26:63.11:620,63,0	0/1:14,15:30:99:370,0,294
+20	10023508	.	GA	G	460.50	.	AC=2;AF=0.50;AN=4;DP=61;Dels=0.46;HRun=11;HaplotypeScore=9.7713;MQ=88.23;MQ0=1;QD=14.85;SB=-189.80;sumGLbyD=16.46	GT:AD:DP:GQ:PL	1/1:12,19:12:52.88:510,53,0	0/0:21,0:20:23.04:0,23,489
+20	10023669	.	GA	G	496.79	.	AC=2;AF=0.50;AN=4;DP=85;Dels=0.26;HRun=11;HaplotypeScore=15.0149;MQ=90.32;MQ0=0;QD=14.19;SB=-256.79;sumGLbyD=15.62	GT:AD:DP:GQ:PL	0/0:50,0:49:95.40:0,95,1160	1/1:13,22:13:61.87:547,62,0
+20	10025820	.	TC	T	381.82	.	AC=2;AF=0.50;AN=4;DP=65;Dels=0.25;HRun=1;HaplotypeScore=7.8208;MQ=83.23;MQ0=4;QD=20.10;SB=-190.53;sumGLbyD=22.72	GT:AD:DP:GQ:PL	0/0:46,0:44:99:0,120,2093	1/1:3,16:0:47.55:432,48,0
+20	10026897	.	T	TA	189.77	.	AC=2;AF=0.50;AN=4;DP=38;Dels=0.00;HRun=8;HaplotypeScore=5.5665;MQ=83.15;MQ0=0;QD=15.81;SB=-97.18;sumGLbyD=19.96	GT:AD:DP:GQ:PL	0/0:26,0:26:54.12:0,54,562	1/1:3,9:12:23:239,23,0
+20	10027761	.	T	TAA	1185.09	.	AC=2;AF=0.50;AN=4;DP=53;Dels=0.00;HRun=0;HaplotypeScore=7.3429;MQ=96.45;MQ0=0;QD=59.25;SB=-568.38;sumGLbyD=61.75	GT:AD:DP:GQ:PL	0/0:33,0:33:89.29:0,89,1077	1/1:1,16:20:54.58:1235,55,0
+20	10036968	.	C	CAAA	354.48	.	AC=3;AF=0.75;AN=4;DP=40;Dels=0.00;HRun=11;HaplotypeScore=4.0302;MQ=77.44;MQ0=1;QD=8.86;SB=-0.00;sumGLbyD=10.03	GT:AD:DP:GQ:PL	0/1:22,1:23:96.54:97,0,232	1/1:10,4:13:18.02:305,18,0
+20	10038289	.	CAA	C	229.65	.	AC=2;AF=0.50;AN=4;DP=44;Dels=0.23;HRun=16;HaplotypeScore=10.5739;MQ=86.96;MQ0=0;QD=5.22;SB=-82.31;sumGLbyD=6.21	GT:AD:DP:GQ:PL	0/1:19,3:19:42.22:42,0,276	0/1:15,5:14:24.06:231,0,24
+20	10041568	.	GT	G	32.14	.	AC=1;AF=0.25;AN=4;DP=178;Dels=0.03;HRun=13;HaplotypeScore=99.6777;MQ=38.37;MQ0=88;QD=0.64;SB=-15.66;sumGLbyD=1.43	GT:AD:DP:GQ:PL	0/1:43,6:20:71.38:71,0,253	0/0:126,0:20:2.40:1,0,250
+20	10044905	.	TA	T	684.30	.	AC=3;AF=0.75;AN=4;DP=49;Dels=0.55;HRun=2;HaplotypeScore=6.7735;MQ=82.97;MQ0=0;QD=13.97;SB=-102.02;sumGLbyD=14.92	GT:AD:DP:GQ:PL	0/1:22,10:22:99:217,0,579	1/1:0,17:0:51.04:514,51,0
+20	10045101	.	C	CTTTT	382.10	.	AC=3;AF=0.75;AN=4;DP=33;Dels=0.00;HRun=10;HaplotypeScore=4.5637;MQ=76.02;MQ0=0;QD=11.58;SB=-102.18;sumGLbyD=12.98	GT:AD:DP:GQ:PL	0/1:12,0:12:6.91:7,0,476	1/1:12,6:21:25.29:422,25,0
+20	10048539	.	CTTCTAG	C	2079.87	.	AC=3;AF=0.75;AN=4;DP=46;Dels=0.63;HRun=0;HaplotypeScore=3.9254;MQ=91.40;MQ0=0;QD=45.21;SB=-843.04;sumGLbyD=46.23	GT:AD:DP:GQ:PL	0/1:13,9:13:99:518,0,828	1/1:4,20:3:59.77:1608,60,0
+20	10049268	.	TAA	T	713.22	.	AC=3;AF=0.75;AN=4;DP=49;Dels=0.47;HRun=7;HaplotypeScore=8.7440;MQ=85.12;MQ0=1;QD=14.56;SB=-335.96;sumGLbyD=15.51	GT:AD:DP:GQ:PL	0/1:24,6:22:99:206,0,1109	1/1:2,17:1:49.97:554,50,0
+20	10049674	.	TTGTGTGTGTGTG	T	514.36	.	AC=1;AF=0.25;AN=4;DP=58;Dels=0.14;HRun=0;HaplotypeScore=12.9192;MQ=71.13;MQ0=10;QD=14.29;SB=-160.31;sumGLbyD=15.55	GT:AD:DP:GQ:PL	0/0:22,0:17:15.05:0,15,459	0/1:28,8:17:1.62:558,3,0
+20	10055047	.	AG	A	384.31	.	AC=1;AF=0.25;AN=4;DP=63;Dels=0.27;HRun=1;HaplotypeScore=6.3278;MQ=88.56;MQ0=0;QD=13.25;SB=-169.84;sumGLbyD=14.70	GT:AD:DP:GQ:PL	0/1:12,17:12:99:426,0,486	0/0:34,0:32:92.56:0,93,1711
+20	10055331	.	G	GTT	1154.63	.	AC=3;AF=0.75;AN=4;DP=59;Dels=0.00;HRun=12;HaplotypeScore=11.0007;MQ=93.08;MQ0=0;QD=19.57;SB=-596.65;sumGLbyD=20.36	GT:AD:DP:GQ:PL	0/1:22,3:26:99:157,0,321	1/1:11,20:31:57.17:1045,57,0
+20	10058726	.	GT	G	519.26	.	AC=3;AF=0.75;AN=4;DP=48;Dels=0.54;HRun=5;HaplotypeScore=3.4082;MQ=90.03;MQ0=0;QD=10.82;SB=-101.29;sumGLbyD=11.79	GT:AD:DP:GQ:PL	0/1:19,8:18:99:132,0,487	1/1:3,18:3:45.97:434,46,0
+20	10062705	.	CA	C	358.95	.	AC=2;AF=0.50;AN=4;DP=60;Dels=0.33;HRun=12;HaplotypeScore=11.1474;MQ=88.71;MQ0=0;QD=5.98;SB=-176.95;sumGLbyD=6.71	GT:AD:DP:GQ:PL	0/1:21,5:20:46.82:47,0,450	0/1:19,15:18:99:356,0,162
+20	10068207	.	C	CAGGCCACAA	477.12	.	AC=2;AF=0.50;AN=4;DP=54;Dels=0.00;HRun=0;HaplotypeScore=26.9189;MQ=93.42;MQ0=0;QD=8.84;SB=-243.75;sumGLbyD=9.65	GT:AD:DP:GQ:PL	0/1:20,1:26:99:245,0,1438	0/1:28,0:28:99:276,0,1441
+20	10069161	.	T	TA	75.14	.	AC=1;AF=0.25;AN=4;DP=73;Dels=0.03;HRun=10;HaplotypeScore=6.3510;MQ=92.42;MQ0=0;QD=2.59;SB=-46.22;sumGLbyD=4.04	GT:AD:DP:GQ:PL	0/0:42,0:42:97.19:0,97,941	0/1:22,6:28:99:117,0,324
+20	10076619	.	CTTTGT	C	980.18	.	AC=1;AF=0.25;AN=4;DP=54;Dels=0.26;HRun=0;HaplotypeScore=6.3555;MQ=89.08;MQ0=0;QD=35.01;SB=-226.12;sumGLbyD=36.51	GT:AD:DP:GQ:PL	0/0:26,0:26:63.22:0,63,1916	0/1:14,14:14:99:1022,0,1081
+20	10078345	.	G	GTA	764.75	.	AC=3;AF=0.75;AN=4;DP=38;Dels=0.00;HRun=0;HaplotypeScore=7.6113;MQ=83.32;MQ0=0;QD=20.13;SB=-141.91;sumGLbyD=21.36	GT:AD:DP:GQ:PL	0/1:14,3:17:99:125,0,213	1/1:8,10:19:30.10:687,30,0

public/testdata/indels.txt

@@ -0,0 +1 @@
+20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	.	AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338