vcf man page
vcf — Variant Call Format The Variant Call Format (VCF) is a TAB-delimited format with each data line consisting of the following fields: The following table gives the INFO tags used by samtools and bcftools. Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele (double) Raw read depth (without quality filtering) (int) # high-quality reference forward bases, ref reverse, alternate for and alt rev bases (int[4]) Consensus quality. Positive: sample genotypes different; negative: otherwise (int) Root-Mean-Square mapping quality of covering reads (int) Phred probability of AF in group1 samples being larger (,smaller) than in group2 (int[2]) Posterior weighted chi^2 P-value between group1 and group2 samples (double) P-value for strand bias, baseQ bias, mapQ bias and tail distance bias (double[4]) Phred-scaled PCHI2 (int) # permutations yielding a smaller PCHI2 (int) Phred log ratio of genotype likelihoods with and without the trio/pair constraint (int) Most probable genotype configuration without the trio constraint (string) Most probable configuration with the trio constraint (string) Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites (float) Mann-Whitney rank-sum test for tail distance bias (float) Hardy-Weinberg equilibrium test (Wigginton et al) (float) The full VCF/BCF file format specification Wigginton JE et al PMID:15789306Description
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) See Also
Info