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Man Pages


Manual Reference Pages  -  VCF (5)

NAME

vcf - Variant Call Format

CONTENTS

Description
See Also

DESCRIPTION

The Variant Call Format (VCF) is a TAB-delimited format with each data line consisting of the following fields:

1CHROMCHROMosome name
2POSthe left-most POSition of the variant
3IDunique variant IDentifier
4REFthe REFerence allele
5ALTthe ALTernate allele(s) (comma-separated)
6QUALvariant/reference QUALity
7FILTERFILTERs applied
8INFOINFOrmation related to the variant (semicolon-separated)
9FORMATFORMAT of the genotype fields (optional; colon-separated)
10+SAMPLESAMPLE 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
Search for    or go to Top of page |  Section 5 |  Main Index


htslib VCF (5) August 2013

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