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- '\" t
- .TH vcf 5 "August 2013" "htslib" "Bioinformatics formats"
- .SH NAME
- vcf \- Variant Call Format
- .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)
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