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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| ##fileformat=VCFv4.2 | ||
| ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | ||
| ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed"> | ||
| ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions for 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=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> | ||
| ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> | ||
| ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled posterior probabilities for genotypes as defined in the VCF specification"> | ||
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=ICNT,Number=2,Type=Integer,Description="Counts of INDEL informative reads based on the reference confidence model"> | ||
| ##FORMAT=<ID=MB,Number=4,Type=Integer,Description="Per-sample component statistics to detect mate bias"> | ||
| ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP 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=PRI,Number=G,Type=Float,Description="Phred-scaled prior probabilities for genotypes"> | ||
| ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> | ||
| ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias"> | ||
| ##FORMAT=<ID=SPL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for SNPs based on the reference confidence model"> | ||
| ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Somatic quality"> | ||
| ##GVCFBlock0-20=minGQ=0(inclusive),maxGQ=20(exclusive) | ||
| ##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive) | ||
| ##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive) | ||
| ##GVCFBlock40-100=minGQ=40(inclusive),maxGQ=100(exclusive) | ||
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | ||
| ##INFO=<ID=AF,Number=A,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=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities"> | ||
| ##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele"> | ||
| ##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> | ||
| ##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality"> | ||
| ##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum"> | ||
| ##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth"> | ||
| ##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations"> | ||
| ##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias"> | ||
| ##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias"> | ||
| ##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format"> | ||
| ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | ||
| ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> | ||
| ##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=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> | ||
| ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | ||
| ##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads"> | ||
| ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> | ||
| ##INFO=<ID=LOD,Number=1,Type=Float,Description="Variant LOD score"> | ||
| ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> | ||
| ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | ||
| ##INFO=<ID=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)"> | ||
| ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> | ||
| ##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score"> | ||
| ##INFO=<ID=R2_5P_bias,Number=1,Type=Float,Description="Score based on mate bias and distance from 5 prime end"> | ||
| ##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele in the following order: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity"> | ||
| ##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."> | ||
| ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | ||
| ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> | ||
| ##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes"> | ||
| ##contig=<ID=chr1,length=248956422> | ||
| ##contig=<ID=chr2,length=242193529> | ||
| ##contig=<ID=chr3,length=198295559> | ||
| ##contig=<ID=chr4,length=190214555> | ||
| ##contig=<ID=chr5,length=181538259> | ||
| ##contig=<ID=chr6,length=170805979> | ||
| ##contig=<ID=chr7,length=159345973> | ||
| ##contig=<ID=chr8,length=145138636> | ||
| ##contig=<ID=chr9,length=138394717> | ||
| ##contig=<ID=chr10,length=133797422> | ||
| ##contig=<ID=chr11,length=135086622> | ||
| ##contig=<ID=chr12,length=133275309> | ||
| ##contig=<ID=chr13,length=114364328> | ||
| ##contig=<ID=chr14,length=107043718> | ||
| ##contig=<ID=chr15,length=101991189> | ||
| ##contig=<ID=chr16,length=90338345> | ||
| ##contig=<ID=chr17,length=83257441> | ||
| ##contig=<ID=chr18,length=80373285> | ||
| ##contig=<ID=chr19,length=58617616> | ||
| ##contig=<ID=chr20,length=64444167> | ||
| ##contig=<ID=chr21,length=46709983> | ||
| ##contig=<ID=chr22,length=50818468> | ||
| ##contig=<ID=chrX,length=156040895> | ||
| ##contig=<ID=chrY,length=57227415> | ||
| ##source=ReblockGVCF | ||
| ##source=SelectVariants | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 | ||
| chrY 2781480 . G <NON_REF> . . END=2790744 GT:DP:GQ 0:11:40 | ||
| chrY 2790745 . A <NON_REF> . . END=2790747 GT:DP:GQ 0:8:0 | ||
| chrY 2790748 . T A,<NON_REF> 73.84 . AS_QUALapprox=|83|0;AS_VarDP=0|8|0;DP=8;MQ=250.00;QUALapprox=83;RAW_GT_COUNT=0,0,1;RAW_MQandDP=500000,8;VarDP=8 GT:AD:AF:DP:F1R2:F2R1:GP:GQ:ICNT:MB:PL:PRI:SB:SPL 1:0,8,0:1.000,0.000:8:0,3,0:0,5,0:7.3841e+01,2.5886e-07,1.9831e+02:74:0,9:0,0,6,2:83,0,173:0.00,9.00,34.77:0,0,3,5:255,0 | ||
| chrY 2790749 . A <NON_REF> . . END=2790749 GT:DP:GQ 0:8:0 |
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