vcf(5) Bioinformatics formats vcf(5)NAMEvcf - Variant Call Format
DESCRIPTION
The Variant Call Format (VCF) is a TAB-delimited format with each data
line consisting of the following fields:
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)
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; nega‐
tive: 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 sam‐
ples (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
htslib August 2013 vcf(5)
