'\" t
.TH vcf 5 "August 2013" "htslib" "Bioinformatics formats"
.SH NAME
vcf \- Variant Call Format
.\"
.\" Copyright (C) 2011 Broad Institute.
.\" Copyright (C) 2013 Genome Research Ltd.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\"
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.SH DESCRIPTION
The Variant Call Format (VCF) is a TAB-delimited format with each data line
consisting of the following fields:
.TS
nlbl.
1	CHROM	CHROMosome name
2	POS	the left-most POSition of the variant
3	ID	unique variant IDentifier
4	REF	the REFerence allele
5	ALT	the ALTernate allele(s) (comma-separated)
6	QUAL	variant/reference QUALity
7	FILTER	FILTERs applied
8	INFO	INFOrmation related to the variant (semicolon-separated)
9	FORMAT	FORMAT of the genotype fields (optional; colon-separated)
10+	SAMPLE	SAMPLE genotypes and per-sample information (optional)
.TE
.P
The following table gives the \fBINFO\fP tags used by samtools and bcftools.
.TP
.B AF1
Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
(double)
.TP
.B DP
Raw read depth (without quality filtering)
(int)
.TP
.B DP4
# high-quality reference forward bases, ref reverse, alternate for and alt rev bases
(int[4])
.TP
.B FQ
Consensus quality. Positive: sample genotypes different; negative: otherwise
(int)
.TP
.B MQ
Root-Mean-Square mapping quality of covering reads
(int)
.TP
.B PC2
Phred probability of AF in group1 samples being larger (,smaller) than in group2
(int[2])
.TP
.B PCHI2
Posterior weighted chi^2 P-value between group1 and group2 samples
(double)
.TP
.B PV4
P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
(double[4])
.TP
.B QCHI2
Phred-scaled PCHI2
(int)
.TP
.B RP
# permutations yielding a smaller PCHI2
(int)
.TP
.B CLR
Phred log ratio of genotype likelihoods with and without the trio/pair constraint
(int)
.TP
.B UGT
Most probable genotype configuration without the trio constraint
(string)
.TP
.B CGT
Most probable configuration with the trio constraint
(string)
.TP
.B VDB
Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites
(float)
.TP
.B RPB
Mann-Whitney rank-sum test for tail distance bias
(float)
.TP
.B HWE
Hardy-Weinberg equilibrium test (Wigginton et al)
(float)
.P
.SH SEE ALSO
.TP
https://github.com/samtools/hts-specs
The full VCF/BCF file format specification
.TP
.I A note on exact tests of Hardy-Weinberg equilibrium
Wigginton JE et al
PMID:15789306
.\" (http://www.ncbi.nlm.nih.gov/pubmed/15789306)