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The Variant Call Format (VCF) Version 4.2 Specification

The Variant Call Format (VCF) Version Specification (Superseded by the VCF Specification introduced in October 2015)23 Aug 2022 The master Version of this document can be found printing is Version 6a6e44a from that repository, last modified on the date shown The VCF specificationVCF is a text file Format (most likely stored in a compressed manner). It contains meta-information lines, a headerline, and then data lines each containing information about a position in the genome. The Format also has the abilityto contain genotype information on samples for each An example##fileformat= ##fileDate=20090805##source= ##reference=file:///seq/ ##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>##phasing=partial##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">##FILTER=<ID=q10,Description="Quality below 10">##FILTER=<ID=s50,Description="Less than 50% of samples have data">## Format =<ID=GT,Number=1,Type=String,Description="Genotype">## Format =<ID=GQ,Number=1,Type=Integer,De scription="G

The URL field specifies the location of a fasta file containing breakpoint assemblies referenced in the VCF records for structural variants via the BKPTID INFO key. 1.2.7 Contig field format As with chromosomal sequences it is highly recommended (but not required) that the header include tags describing the contigs referred to in the VCF file.

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The Variant Call Format (VCF) Version 4.2 Specification

samtools.github.io

1.2.7 Contig field format As with chromosomal sequences it is highly recommended (but not required) that the header include tags describing the contigs referred to in the VCF file. This furthermore allows these contigs to come from different files. The format

  Contig

Sequence Alignment/Map Format Speci cation

samtools.github.io

1.3 The header section Each header line begins with the character ‘@’ followed by one of the two-letter header record type codes de ned in this section.

  Format

Sequence Alignment/Map Format Specification

samtools.github.io

Template A DNA/RNA sequence part of which is sequenced on a sequencing machine or assembled from raw sequences. Segment A contiguous sequence or subsequence. Read A raw sequence that comes off a sequencing machine. A read may consist of multiple segments. For sequencing data, reads are indexed by the order in which they are sequenced.

  Specification, Template

The Variant Call Format (VCF) Version 4.1 Specification

samtools.github.io

encouraged to use the rs number(s). No identifier should be present in more than one data record. If there is no identifier available, then the missing value should be used. (String, no whitespace or semicolons permitted) 4. REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted.

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