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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)

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