vcf man page

vcf ā€” Variant Call Format

Description

The Variant Call Format (VCF) is a TAB-delimited format with each data line consisting of the following fields:

1CHROMCHROMosome name
2POSthe left-most POSition of the variant
3IDunique variant IDentifier
4REFthe REFerence allele
5ALTthe ALTernate allele(s) (comma-separated)
6QUALvariant/reference QUALity
7FILTERFILTERs applied
8INFOINFOrmation related to the variant (semicolon-separated)
9FORMATFORMAT of the genotype fields (optional; colon-separated)
10+SAMPLESAMPLE genotypes and per-sample information (optional)

The following table gives the INFO tags used by samtools and bcftools.

AF1

Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele (double)

DP

Raw read depth (without quality filtering) (int)

DP4

# high-quality reference forward bases, ref reverse, alternate for and alt rev bases (int[4])

FQ

Consensus quality. Positive: sample genotypes different; negative: otherwise (int)

MQ

Root-Mean-Square mapping quality of covering reads (int)

PC2

Phred probability of AF in group1 samples being larger (,smaller) than in group2 (int[2])

PCHI2

Posterior weighted chi^2 P-value between group1 and group2 samples (double)

PV4

P-value for strand bias, baseQ bias, mapQ bias and tail distance bias (double[4])

QCHI2

Phred-scaled PCHI2 (int)

RP

# permutations yielding a smaller PCHI2 (int)

CLR

Phred log ratio of genotype likelihoods with and without the trio/pair constraint (int)

UGT

Most probable genotype configuration without the trio constraint (string)

CGT

Most probable configuration with the trio constraint (string)

VDB

Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites (float)

RPB

Mann-Whitney rank-sum test for tail distance bias (float)

HWE

Hardy-Weinberg equilibrium test (Wigginton et al) (float)

See Also

https://github.com/samtools/hts-specs

The full VCF/BCF file format specification

A note on exact tests of Hardy-Weinberg equilibrium

Wigginton JE et al PMID:15789306

Info

August 2013 htslib Bioinformatics formats