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December 9, 2015 01:02
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bcftools merge 3rd sample missing
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| ##fileformat=VCFv4.1 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present"> | |
| ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3"> | |
| ##FILTER=<ID=nc,Description="No-call"> | |
| ##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens"> | |
| ##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | |
| ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| ##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping"> | |
| ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping"> | |
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | |
| ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend"> | |
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele"> | |
| ##INFO=<ID=CGA_XR,Number=A,Type=String,Description="Per-ALT external database reference (dbSNP, COSMIC, etc)"> | |
| ##INFO=<ID=CGA_BF,Number=1,Type=Float,Description="Frequency in baseline"> | |
| ##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record"> | |
| ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block"> | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G06 | |
| chr1 10107 . C . 0.00 LowGQX;HighDPFRatio END=10110;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:1 | |
| ##fileformat=VCFv4.1 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present"> | |
| ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3"> | |
| ##FILTER=<ID=nc,Description="No-call"> | |
| ##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens"> | |
| ##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | |
| ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| ##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping"> | |
| ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping"> | |
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | |
| ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend"> | |
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele"> | |
| ##INFO=<ID=CGA_XR,Number=A,Type=String,Description="Per-ALT external database reference (dbSNP, COSMIC, etc)"> | |
| ##INFO=<ID=CGA_BF,Number=1,Type=Float,Description="Frequency in baseline"> | |
| ##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record"> | |
| ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block"> | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT D05 | |
| chr1 10106 . C . 0.00 LowGQX END=10107;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:12:5:0 | |
| ##fileformat=VCFv4.1 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present"> | |
| ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3"> | |
| ##FILTER=<ID=nc,Description="No-call"> | |
| ##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens"> | |
| ##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | |
| ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| ##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping"> | |
| ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping"> | |
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | |
| ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend"> | |
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele"> | |
| ##INFO=<ID=CGA_XR,Number=A,Type=String,Description="Per-ALT external database reference (dbSNP, COSMIC, etc)"> | |
| ##INFO=<ID=CGA_BF,Number=1,Type=Float,Description="Frequency in baseline"> | |
| ##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record"> | |
| ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block"> | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H09 | |
| chr1 10107 . C . 0.00 LowGQX END=10120;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:5:2:0 | |
| MERGE RESULTS: | |
| ##fileformat=VCFv4.1 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present"> | |
| ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3"> | |
| ##FILTER=<ID=nc,Description="No-call"> | |
| ##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens"> | |
| ##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | |
| ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| ##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping"> | |
| ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping"> | |
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | |
| ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | |
| ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakend"> | |
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele"> | |
| ##INFO=<ID=CGA_XR,Number=A,Type=String,Description="Per-ALT external database reference (dbSNP, COSMIC, etc)"> | |
| ##INFO=<ID=CGA_BF,Number=1,Type=Float,Description="Frequency in baseline"> | |
| ##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record"> | |
| ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block"> | |
| ##contig=<ID=chr1> | |
| ##bcftools_mergeVersion=1.2-190-g71921ca+htslib-1.2.1-226-g1e5c377 | |
| ##bcftools_mergeCommand=merge test1.gz test2.gz test3.gz | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G06 D05 H09 | |
| chr1 10106 . C . 0 LowGQX END=10107;BLOCKAVG_min30p3a;AN=2 GT:GQX:DP:DPF ./.:.:.:. 0/0:12:5:0 ./.:.:.:. | |
| chr1 10107 . C . 0 LowGQX;HighDPFRatio END=10110;BLOCKAVG_min30p3a;AN=2 GT:GQX:DP:DPF .:.:0:1 ./.:.:.:. 0/0:5:2:0 |
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