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vcf(5)                      Bioinformatics formats                      vcf(5)

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

htslib                            August 2013                           vcf(5)