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vcf(5)			    Bioinformatics formats			vcf(5)

       vcf - Variant Call Format

       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;	 nega-
	      tive: 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  sam-
	      ples (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

       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)

	      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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