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Handle trailing reference blocks in CombineGVCFs. (#4615)
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47 changes: 47 additions & 0 deletions
47
...itute/hellbender/tools/walkers/CombineGVCFs/gvcfExample1WithTrailingReferenceBlocks.g.vcf
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##fileformat=VCFv4.1 | ||
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | ||
##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="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> | ||
##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block"> | ||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | ||
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> | ||
##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) | ||
##INFO=<ID=BLOCK_SIZE,Number=1,Type=Integer,Description="Size of the homozygous reference GVCF block"> | ||
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | ||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | ||
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | ||
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most 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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | ||
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | ||
##contig=<ID=chr20,length=64444167> | ||
##contig=<ID=chr21,length=46709983> | ||
##contig=<ID=chr20_GL383577v2_alt,length=128386> | ||
##contig=<ID=chr20_KI270869v1_alt,length=118774> | ||
##contig=<ID=chr20_KI270871v1_alt,length=58661> | ||
##contig=<ID=chr20_KI270870v1_alt,length= 183433> | ||
##contig=<ID=chr21_GL383578v2_alt,length=63917> | ||
##contig=<ID=chr21_KI270874v1_alt,length= 166743> | ||
##contig=<ID=chr21_KI270873v1_alt,length=143900> | ||
##contig=<ID=chr21_GL383579v2_alt,length=201197> | ||
##contig=<ID=chr21_GL383580v2_alt,length=74653> | ||
##contig=<ID=chr21_GL383581v2_alt,length=116689> | ||
##contig=<ID=chr21_KI270872v1_alt,length=82692> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 | ||
chr20 69491 . G <NON_REF> . . BLOCK_SIZE=20;END=69510 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:94:99:82:99:0,120,1800 | ||
chr20 69511 . A G,<NON_REF> 2253.77 . BaseQRankSum=1.169;DP=82;MQ=31.05;MQ0=0;MQRankSum=-0.866;ReadPosRankSum=1.689 GT:AD:DP:GQ:PL:SB 1/1:1,79,0:80:99:2284,207,0,2287,237,2316:0,1,46,33 | ||
chr20 69512 . C <NON_REF> . . BLOCK_SIZE=10;END=69521 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:96:99:82:99:0,120,1800 | ||
chr20 69522 . T <NON_REF> . . BLOCK_SIZE=27;END=69548 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:95:0:95:0:0,0,0 | ||
chr20 69549 . G <NON_REF> . . BLOCK_SIZE=86;END=69634 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:156:99:56:66:0,66,990 | ||
chr20 69635 . G T,<NON_REF> 60.77 . BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754 GT:AD:DP:GQ:PL:SB 0/1:4,3,0:7:89:89,0,119,101,128,229:0,4,0,3 | ||
chr20 69762 . T <NON_REF> . . BLOCK_SIZE=1;END=69762 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:18:7:18:0,18,270 | ||
chr20 69763 . A <NON_REF> . . BLOCK_SIZE=4;END=69766 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:21:7:21:0,21,253 | ||
chr20 69767 . C <NON_REF> . . BLOCK_SIZE=5;END=69771 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:12:7:12:0,12,180 | ||
chr20 69772 . AAAGC A,<NON_REF> 60.77 . BaseQRankSum=0.937;DP=7;MQ=34.15;MQ0=0;MQRankSum=1.300;ReadPosRankSum=1.754 GT:AD:DP:GQ:PL:SB 0/1:4,3,0:7:89:89,0,119,101,128,229:0,4,0,3 | ||
chr20 69773 . A <NON_REF> . . BLOCK_SIZE=10;END=69783 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:0:3:0:0,0,0 | ||
chr21 1 . G <NON_REF> . . END=46709983 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 | ||
chr20_GL383577v2_alt 1 . G <NON_REF> . . END=128386 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 |
41 changes: 41 additions & 0 deletions
41
...itute/hellbender/tools/walkers/CombineGVCFs/gvcfExample2WithTrailingReferenceBlocks.g.vcf
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##fileformat=VCFv4.1 | ||
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | ||
##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="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> | ||
##FORMAT=<ID=MIN_GQ,Number=1,Type=Integer,Description="Minimum GQ observed within the GVCF block"> | ||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | ||
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> | ||
##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) | ||
##INFO=<ID=BLOCK_SIZE,Number=1,Type=Integer,Description="Size of the homozygous reference GVCF block"> | ||
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | ||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | ||
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | ||
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most 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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | ||
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | ||
##contig=<ID=chr20,length=64444167> | ||
##contig=<ID=chr21,length=46709983> | ||
##contig=<ID=chr20_GL383577v2_alt,length=128386> | ||
##contig=<ID=chr20_KI270869v1_alt,length=118774> | ||
##contig=<ID=chr20_KI270871v1_alt,length=58661> | ||
##contig=<ID=chr20_KI270870v1_alt,length= 183433> | ||
##contig=<ID=chr21_GL383578v2_alt,length=63917> | ||
##contig=<ID=chr21_KI270874v1_alt,length= 166743> | ||
##contig=<ID=chr21_KI270873v1_alt,length=143900> | ||
##contig=<ID=chr21_GL383579v2_alt,length=201197> | ||
##contig=<ID=chr21_GL383580v2_alt,length=74653> | ||
##contig=<ID=chr21_GL383581v2_alt,length=116689> | ||
##contig=<ID=chr21_KI270872v1_alt,length=82692> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA2 | ||
chr20 69498 . C <NON_REF> . . BLOCK_SIZE=9;END=69506 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:94:99:82:99:0,120,1800 | ||
chr20 69514 . T <NON_REF> . . BLOCK_SIZE=111;END=69624 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:96:99:82:99:0,120,1800 | ||
chr20 69625 . A <NON_REF> . . BLOCK_SIZE=51;END=69675 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:18:7:18:0,18,270 | ||
chr20 69767 . C <NON_REF> . . BLOCK_SIZE=8;END=69774 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:12:7:15:0,12,180 | ||
chr20 69775 . C <NON_REF> . . BLOCK_SIZE=17;END=69791 GT:DP:GQ:MIN_DP:MIN_GQ:PL 0/0:7:15:7:15:0,15,160 | ||
chr21 1 . G <NON_REF> . . END=46709983 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 | ||
chr20_GL383577v2_alt 1 . G <NON_REF> . . END=128386 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 |
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