More testdata test files
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Mark DePristo
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##fileformat=VCFv4.1
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
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##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DB,Number=1,Type=Integer,Description="dbSNP membership">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
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##UG_assume_single_sample_reads=null
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##UG_base_model=EMPIRICAL
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##UG_genotype=false
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##UG_genotype_model=JOINT_ESTIMATE
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##UG_heterozygosity=0.0010
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##UG_include_experimental_annotations=false
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##UG_max_deletion_fraction=0.05
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##UG_max_mismatches_in_40bp_window=3
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##UG_min_base_quality_score=10
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##UG_min_confidence_threshold=50.0
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##UG_min_mapping_quality_score=10
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##UG_noSLOD=false
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##UG_output_all_callable_bases=false
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##UG_platform=SOLID
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##UG_poolSize=0
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##UG_use_reads_with_bad_mates=false
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##VariantsToVCF="analysis_type=VariantsToVCF input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/Users/depristo/Desktop/broadLocal/localData/human_b36_both.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false useSlowGenotypes=false repairVCFHeader=null logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub variant=(RodBinding name=variant source=3.3.vcf) dbsnp=(RodBinding name= source=UNBOUND) sample=null fixRef=false filter_mismatching_base_and_quals=false"
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##reference=file:///Users/depristo/Desktop/broadLocal/localData/human_b36_both.fasta
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##source=UnifiedGenotyper
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA19238 NA19239 NA19240
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1 241 . T A 93.16 . AB=0.82;AC=1;AF=0.17;AN=6;DB=0;DP=1092;Dels=0.00;HRun=2;MQ=42.08;MQ0=759;QD=0.39;SB=-90.62 GT:DP:GQ 1/0:.:99 0/0:.:99 0/0:.:30
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1 327 . T C 666.18 . AB=0.74;AC=3;AF=0.50;AN=6;DB=0;DP=936;Dels=0.00;HRun=3;MQ=34.66;MQ0=728;QD=0.71;SB=-268.74 GT:DP:GQ 1/0:.:63 1/0:.:99 1/0:.:99
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1 463 . A C 60.79 . AB=0.97;AC=1;AF=0.17;AN=6;DB=0;DP=571;Dels=0.00;HRun=0;MQ=56.66;MQ0=480;QD=0.23;SB=-66.13 GT:DP:GQ 0/0:.:37 0/0:.:1 0/1:.:93
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1 469 . C G 439 . AB=0.66;AC=2;AF=0.33;AN=6;DB=0;DP=120;Dels=0.00;HRun=1;MQ=136.52;MQ0=19;QD=4.18;SB=-201.52 GT:DP:GQ 0/1:.:99 0/0:.:15 0/1:.:99
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1 492 rs55998931 C T 55.01 . AB=0.79;AC=2;AF=0.33;AN=6;DB=1;DP=97;Dels=0.00;HRun=0;MQ=128.37;MQ0=4;QD=1.83;SB=-55.42 GT:DP:GQ 0/1:.:56 0/1:.:36 0/0:.:99
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1 603 . G A 182.34 . AB=0.80;AC=2;AF=0.33;AN=6;DB=0;DP=97;Dels=0.00;HRun=1;MQ=74.14;MQ0=42;QD=2.40;SB=-27.00 GT:DP:GQ 1/0:.:40 0/0:.:6 1/0:.:99
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1 4770 rs6682375 A G 301.23 . AB=0.64;AC=4;AF=0.67;AN=6;DB=1;DP=186;Dels=0.00;HRun=1;MQ=30.01;MQ0=130;QD=1.62;SB=-142.86 GT:DP:GQ 1/1:.:10 0/1:.:99 0/1:.:99
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1 4793 rs6682385 A G 1687.16 . AB=0.54;AC=3;AF=0.50;AN=6;DB=1;DP=242;Dels=0.00;HRun=0;MQ=77.94;MQ0=43;QD=6.97;SB=-891.19 GT:DP:GQ 0/1:.:5 0/1:.:99 0/1:.:99
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1 6120 rs11489794 G C 67.12 . AB=0.89;AC=1;AF=0.17;AN=6;DB=1;DP=381;Dels=0.00;HRun=0;MQ=87.38;MQ0=91;QD=0.35;SB=-46.61 GT:DP:GQ 0/0:.:7 0/0:.:21 1/0:.:99
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1 6358 rs3210724 G C 161.57 . AB=0.77;AC=3;AF=0.50;AN=6;DB=1;DP=172;Dels=0.00;HRun=0;MQ=28.74;MQ0=146;QD=0.94;SB=-114.42 GT:DP:GQ 1/0:.:49 1/0:.:25 1/0:.:93
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1 9117 rs11525710 G C 118.91 . AB=0.88;AC=2;AF=0.33;AN=6;DB=1;DP=238;Dels=0.00;HRun=0;MQ=34.51;MQ0=158;QD=1.05;SB=-30.35 GT:DP:GQ 1/0:.:24 1/0:.:99 0/0:.:87
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1 9992 rs12354148 C T 204.73 . AB=0.85;AC=2;AF=0.33;AN=6;DB=1;DP=416;Dels=0.00;HRun=0;MQ=86.33;MQ0=75;QD=1.07;SB=-64.25 GT:DP:GQ 0/1:.:74 0/1:.:99 0/0:.:99
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1 9993 rs7354882 G A 494.64 . AB=0.86;AC=2;AF=0.33;AN=6;DB=1;DP=414;Dels=0.00;HRun=0;MQ=86.54;MQ0=73;QD=1.69;SB=-92.13 GT:DP:GQ 1/0:.:99 0/0:.:99 1/0:.:99
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1 18239 rs11489791 G A 123.67 . AC=6;AF=1.00;AN=6;DB=1;DP=128;Dels=0.00;HRun=1;MQ=4.20;MQ0=123;QD=0.97;SB=-30.00 GT:DP:GQ 1/1:.:3 1/1:.:9 1/1:.:3
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1 20748 . T C 131.72 . AB=0.84;AC=2;AF=0.33;AN=6;DB=0;DP=168;Dels=0.00;HRun=1;MQ=30.37;MQ0=101;QD=1.02;SB=-82.00 GT:DP:GQ 0/0:.:27 1/0:.:37 1/0:.:99
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