NAME

       vcf - 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; 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