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denisemauldin/VCF_examples

Created October 30, 2015 00:02
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Examples for bcftools error message.
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VCF_examples
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##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">
##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">
##FILTER=<ID=nc,Description="No-call">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 15031
chrM 11 7_L C [M:157[NC . PASS NS=1;SVTYPE=BND;MATEID=7_R;CGA_BF=0 GT 1
chrM 73 rs3087742 A G . PASS NS=1;AN=1;AC=1;CGA_XR=dbsnp.102|rs3087742;CGA_FI=4535|-|ND1|TSS-UPSTREAM|UNKNOWN-INC&4536|-|ND2|TSS-UPSTREAM|UNKNOWN-INC&4549|-|RNR1|TSS-UPSTREAM|UNKNOWN-INC&4558|-|TRNF|TSS-UPSTREAM|UNKNOWN-INC&4565|-|TRNI|TSS-UPSTREAM|UNKNOWN-INC&4567|-|TRNL1|TSS-UPSTREAM|UNKNOWN-INC&4569|-|TRNM|TSS-UPSTREAM|UNKNOWN-INC&4577|-|TRNV|TSS-UPSTREAM|UNKNOWN-INC GT:GQ:HQ:EHQ 1:6194:6194,.:6194,.
##fileformat=VCFv4.1
##contig=<ID=chrM,length=16571>
##contig=<ID=chrY,length=59373566>
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=nc,Description="No-call">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.999 or higher that read contains indicated allele vs all other intersecting indel alleles)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="CGI:Total Read Depth;ILMN:Filtered basecall depth used for site genotyping">
##INFO=<ID=SNVSB,Number=1,Type=Float,Description="SNV site strand bias">
##INFO=<ID=SNVHPOL,Number=1,Type=Integer,Description="SNV contextual homopolymer length">
##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">
##INFO=<ID=CSQ,Number=1,Type=String,Description="Consequence type as predicted by VEP v2.4. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|PolyPhen|SIFT|CANONICAL|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|Condel">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B02
chrM 1 . G . 0 nc . GT:GQX:DP:DPF 0/0:10:4:0
chrM 72 . T . 0 nc . GT:GQX:DP:DPF 0/0:859:287:477
chrM 73 . G A 3070 PASS SNVSB=-74.9;SNVHPOL=3;CSQ=A|ENSG00000198763|ENST00000361453|Transcript|5KB_upstream_variant|||||||||YES|MT-ND2|||||,A|ENSG00000210077|ENST00000387342|Transcript|2KB_upstream_variant|||||||||YES||||||,A|ENSG00000198888|ENST00000361390|Transcript|5KB_upstream_variant|||||||||YES|MT-ND1|||||,A|ENSG00000210049|ENST00000387314|Transcript|2KB_upstream_variant|||||||||YES||||||,A|ENSG00000210107|ENST00000387372|Transcript|5KB_downstream_variant|||||||||YES||||||,A|ENSG00000209082|ENST00000386347|Transcript|5KB_upstream_variant|||||||||YES||||||,A|ENSG00000211459|ENST00000389680|Transcript|2KB_upstream_variant|||||||||YES||||||,A|ENSG00000210082|ENST00000387347|Transcript|2KB_upstream_variant|||||||||YES|MIR4485|||||,A|ENSG00000210112|ENST00000387377|Transcript|5KB_upstream_variant|||||||||YES||||||,A|ENSG00000210100|ENST00000387365|Transcript|5KB_upstream_variant|||||||||YES|||||| GT:GQ:GQX:DP:DPF:AD 1/1:1730:1730:577:186:0,577
chrY 1 . N . 0 nc END=2918335;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0
##fileformat=VCFv4.1
##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=nc,Description="No-call">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##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_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">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=EHQ,Number=2,Type=Integer,Description="Haplotype Quality, Equal Allele Fraction Assumption">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 15032
chrM 73 rs3087742 A G . PASS NS=1;AN=1;AC=1;CGA_XR=dbsnp.102|rs3087742;CGA_FI=4535|-|ND1|TSS-UPSTREAM|UNKNOWN-INC&4536|-|ND2|TSS-UPSTREAM|UNKNOWN-INC&4549|-|RNR1|TSS-UPSTREAM|UNKNOWN-INC&4558|-|TRNF|TSS-UPSTREAM|UNKNOWN-INC&4565|-|TRNI|TSS-UPSTREAM|UNKNOWN-INC&4567|-|TRNL1|TSS-UPSTREAM|UNKNOWN-INC&4569|-|TRNM|TSS-UPSTREAM|UNKNOWN-INC&4577|-|TRNV|TSS-UPSTREAM|UNKNOWN-INC GT:GQ:HQ:EHQ 1:6104:6104,.:6104,.
chrY 1 . N . . nc END=10000;NS=1;AN=0 GT .
chrY 10001 . C . . nc END=2649519;NS=1;AN=0 GT .
chrY 2649520 . A . . nc NS=1;AN=0 GT .
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