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gatk-3.8/public/testdata/inttestbgl.output.vcf

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##fileformat=VCFv4.0
##FILTER=<ID=FDRtranche12.50to25.00,Description="FDR tranche level at qual 1.8">
##FILTER=<ID=FDRtranche25.00to35.00+,Description="FDR tranche level at qual > 4.8">
##FILTER=<ID=FDRtranche5.00to12.50,Description="FDR tranche level at qual 4.8">
##FILTER=<ID=HARD_TO_VALIDATE,Description="(MQ0 / (1.0 * DP)) > 0.1">
##FILTER=<ID=InDel,Description="Overlaps a user-input mask">
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
##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">
##FORMAT=<ID=OG,Number=1,Type=String,Description="Original Genotype input to Beagle">
##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DB,Number=1,Type=Integer,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=NumGenotypesChanged,Number=1,Type=Integer,Description="r2 Value reported by Beagle on each site">
##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=R2,Number=1,Type=Float,Description="r2 Value reported by Beagle on each site">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##UG_assume_single_sample_reads=null
##UG_bam_file_used=CEUTSI.chr20.cleaned.bam
##UG_base_model=EMPIRICAL
##UG_cap_base_quality_by_mapping_quality=false
##UG_genotype=false
##UG_genotype_model=JOINT_ESTIMATE
##UG_heterozygosity=0.0010
##UG_max_deletion_fraction=0.05
##UG_max_mismatches_in_40bp_window=3
##UG_min_base_quality_score=10
##UG_min_mapping_quality_score=10
##UG_noSLOD=false
##UG_output_all_callable_bases=false
##UG_platform=null
##UG_standard_min_confidence_threshold_for_calling=10.0
##UG_standard_min_confidence_threshold_for_emitting=30.0
##UG_trigger_min_confidence_threshold_for_calling=30.0
##UG_trigger_min_confidence_threshold_for_emitting=30.0
##UG_use_reads_with_bad_mates=false
##reference=human_g1k_v37.fasta
##source=BeagleImputation
##source=UnifiedGenotyper
##source=VariantOptimizer
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA07056 NA11892 NA11893 NA12347 NA12348 NA12383 NA12413 NA12546 NA12775 NA12777 NA12778 NA20502 NA20505 NA20508 NA20509 NA20510 NA20512 NA20515 NA20516 NA20517 NA20518 NA20519 NA20520 NA20522 NA20524 NA20525 NA20527 NA20528 NA20529 NA20530 NA20531 NA20534 NA20535 NA20538 NA20539 NA20540 NA20541 NA20542 NA20543 NA20544 NA20582 NA20586 NA20588 NA20589 NA20752 NA20753 NA20754 NA20755 NA20756
20 60864 . G C 20.43 PASS AB=0.60;AC=1;AF=0.01;AN=98;DB=0;DP=200;Dels=0.00;HRun=0;HaplotypeScore=29.58;MQ=57.91;MQ0=0;NumGenotypesChanged=2;OQ=25.61;QD=5.12;R2=0.815;SB=-529.44 GT:DP:GL:GQ:OG 0|0:5:-0.00,-1.51,-21.02:30.97 0|0:5:-0.00,-1.51,-20.93:30.97 0|0:4:-0.00,-1.21,-16.78:27.99 0|0:3:-0.00,-0.90,-12.59:24.89 0|0:6:-0.00,-1.81,-23.82:33.98 0|0:3:-0.00,-0.90,-12.49:24.89 0|0:2:-0.00,-0.60,-8.38:21.90 0|0:7:-0.05,-2.15,-26.86:36.78 0|0:4:-0.00,-1.21,-15.43:27.99 0|0:10:-0.02,-3.03,-39.69:45.23 0|0:3:-0.00,-0.91,-11.93:24.99 0|0:1:-0.00,-0.30,-4.29:18.93 0|0:.:0,0,0:15.96:./. 0|0:5:-0.00,-1.51,-20.53:30.97 0|0:2:-0.00,-0.60,-8.24:21.90 0|0:1:-0.00,-0.30,-4.19:18.93 0|0:4:-0.00,-1.21,-16.63:27.99 0|0:5:-0.01,-1.51,-17.93:30.86 0|0:1:-0.00,-0.30,-4.29:18.93 0|0:2:-0.00,-0.60,-7.94:21.90 0|0:5:-0.00,-1.51,-22.56:30.97 0|0:9:-0.01,-2.71,-35.06:43.01 0|0:8:-0.00,-2.41,-33.10:40 0|0:2:-0.00,-0.60,-7.94:21.90 0|0:2:-0.00,-0.60,-8.24:21.90 0|0:6:-0.01,-1.81,-22.97:33.87 0|0:3:-0.00,-0.90,-12.63:24.89 0|0:6:-0.03,-1.83,-20.97:33.87 1|0:5:-7.64,-1.51,-11.93:60 0|0:4:-0.00,-1.21,-17.12:27.99 0|0:7:-0.02,-2.13,-26.26:36.99 0|0:3:-0.00,-0.90,-11.79:24.89 0|0:3:-0.00,-0.91,-11.98:24.99 0|0:.:0,0,0:15.96:./. 0|0:8:-0.00,-2.41,-33.55:40 0|0:3:-0.00,-0.90,-12.63:24.89 0|0:1:-0.00,-0.30,-3.75:18.93 0|0:2:-0.00,-0.61,-6.79:22.01 0|0:5:-0.00,-1.51,-19.13:30.97 0|0:1:-0.00,-0.30,-3.55:18.93 0|0:1:-0.00,-0.30,-3.65:18.93 0|0:3:-0.01,-0.91,-11.19:24.89 0|0:5:-0.00,-1.51,-19.13:30.97 0|0:3:-0.00,-0.90,-12.83:24.89 0|0:2:-0.00,-0.60,-7.79:21.90 0|0:4:-0.00,-1.21,-15.58:27.99 0|0:4:-0.01,-1.21,-15.48:27.88 0|0:5:-0.00,-1.51,-20.43:30.97 0|0:5:-0.01,-1.52,-19.02:30.97
20 61098 rs6078030 C T 35.52 PASS AB=0.52;AC=10;AF=0.10;AN=98;DB=1;DP=160;Dels=0.01;HRun=1;HaplotypeScore=43.51;MQ=52.70;MQ0=0;NumGenotypesChanged=5;OQ=365.15;QD=10.14;R2=0.644;SB=-566.38 GT:DP:GL:GQ:OG 0|0:.:0,0,0:16.41:./. 0|0:4:-0.00,-1.20,-13.17:28.51 0|0:2:-0.00,-0.60,-6.76:22.77 0|0:4:-0.01,-1.21,-12.78:26.31 0|0:5:-0.01,-1.51,-15.00:29.67 0|0:1:-0.00,-0.30,-3.40:6.11 0|1:4:-7.95,-1.21,-5.27:60 0|0:4:-0.05,-1.23,-10.60:13.87 0|0:3:-0.00,-0.90,-9.46:25.48 0|1:7:-3.17,-2.11,-19.85:11.80 0|0:7:-0.05,-2.14,-21.69:37.45 0|0:2:-0.00,-0.60,-6.16:20.58 0|0:1:-0.00,-0.30,-2.97:5.99 0|0:4:-0.00,-1.21,-13.96:16.95 0|0:5:-0.00,-1.51,-17.03:30.18 0|0:4:-0.00,-1.21,-13.23:27.99 0|0:4:-0.00,-1.21,-13.43:27.06 0|0:3:-0.00,-0.90,-9.53:25.90 0|0:.:0,0,0:4.13:./. 0|0:1:-0.00,-0.30,-3.50:19.59 1|1:1:-3.16,-0.30,-0.00:1.79 0|0:6:-0.01,-1.81,-18.42:20.08 0|1:10:-16.43,-3.02,-15.44:60 0|0:2:-0.00,-0.60,-6.56:22.65 0|0:2:-0.00,-0.60,-5.44:12.36 0|0:1:-0.00,-0.30,-3.50:6.34 0|0:2:-0.00,-0.60,-5.34:22.85 0|0:2:-0.00,-0.60,-5.74:8.81 0|0:2:-0.00,-0.60,-6.16:9.07 0|0:4:-0.00,-1.21,-14.18:14.73 0|0:3:-0.00,-0.90,-9.96:11.29 0|0:2:-0.00,-0.60,-6.49:22.89 0|0:2:-0.00,-0.60,-6.39:22.28 0|0:.:0,0,0:4.13:./. 0|0:2:-0.00,-0.60,-6.19:13.40 0|0:2:-0.00,-0.60,-5.64:8.34 1|0:3:-2.77,-0.91,-6.17:16.46 0|0:2:-0.00,-0.60,-6.09:21.67 0|1:2:-3.89,-0.61,-1.57:26.88 0|0:4:-0.01,-1.21,-11.76:28.54 1|0:3:-3.07,-0.60,-2.97:22.03 0|0:.:0,0,0:3.76:./. 0|0:3:-0.00,-0.90,-9.66:11.29 0|0:1:-0.00,-0.30,-3.70:16.60 0|0:.:0,0,0:3.84:./. 1|0:4:-7.02,-1.21,-6.79:60 1|0:2:-3.67,-0.60,-3.40:29 0|0:6:-0.00,-1.81,-20.38:19.90 0|0:8:-0.01,-2.41,-26.64:25.87
20 61421 . A C 30.89 PASS AC=2;AF=0.02;AN=98;DB=0;DP=195;Dels=0.00;HRun=0;HaplotypeScore=13.83;MQ=35.59;MQ0=44;NumGenotypesChanged=7;OQ=21.62;QD=7.21;R2=0.655;SB=-470.00 GT:DP:GL:GQ:OG 0|0:3:-0.00,-0.90,-10.42:32.52 0|0:5:-0.00,-1.51,-18.21:38.86 0|0:1:-0.00,-0.30,-3.79:27.10 0|0:3:-0.00,-0.90,-10.32:30.04 0|0:3:-0.00,-0.90,-9.77:30.36 0|0:5:-0.00,-1.51,-16.15:24.21 0|0:4:-0.00,-1.20,-14.67:33.98 0|0:5:-0.00,-1.51,-16.76:23.25 0|0:.:0,0,0:23.73:./. 0|0:5:-0.00,-1.51,-17.21:22.93 0|0:5:-0.00,-1.51,-19.02:38.86 0|0:5:-0.01,-1.51,-14.79:36.38 0|0:1:-0.00,-0.30,-3.14:11.83 0|0:3:-0.00,-0.90,-10.83:20.11 0|1:1:-3.06,-0.30,-0.00:18.23:1/1 0|0:1:-0.00,-0.30,-3.69:25.95 0|0:1:-0.00,-0.30,-3.69:24.78 0|0:3:-0.00,-0.90,-9.53:33.28 0|0:2:-0.00,-0.60,-6.28:16.14 0|0:2:-0.00,-0.60,-6.59:29.83 0|0:2:-0.00,-0.60,-6.58:16.67 0|0:2:-0.00,-0.60,-6.58:14.17 0|0:3:-0.01,-0.91,-8.92:17.19 0|0:2:-0.00,-0.60,-6.43:29.91 0|0:3:-0.00,-0.90,-9.93:21.63 0|0:1:-0.00,-0.30,-3.44:12.38 0|0:1:-0.00,-0.30,-3.59:27.24 0|0:1:-0.00,-0.30,-3.44:11.88 0|0:.:0,0,0:9.15:./. 0|0:.:0,0,0:8.74:./. 0|0:3:-0.00,-0.90,-10.17:17.36 0|0:3:-0.00,-0.90,-9.72:33.28 0|0:2:-0.00,-0.60,-6.33:29.43 0|0:2:-0.00,-0.60,-6.18:16.14 0|0:3:-0.00,-0.90,-9.22:22.80 0|0:1:-0.00,-0.30,-2.64:11.32 0|0:.:0,0,0:16.07:./. 0|0:3:-0.00,-0.90,-10.02:31.61 0|0:1:-0.00,-0.30,-3.34:24.80 0|0:2:-0.00,-0.60,-7.13:29.79 0|1:1:-2.96,-0.30,-0.00:17.54:1/1 0|0:1:-0.00,-0.30,-3.24:12.49 0|0:3:-0.00,-0.90,-9.72:17.36 0|0:.:0,0,0:20.13:./. 0|0:1:-0.01,-0.30,-2.14:12.53 0|0:4:-0.00,-1.20,-13.31:34.56 0|0:5:-0.00,-1.51,-17.05:36.99 0|0:2:-0.00,-0.60,-6.63:13.91 0|0:5:-0.00,-1.51,-16.95:23.08
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