Man page - popstats(1)

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Manual

POPSTATS

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

NAME

popStats

SYNOPSIS

popStat –type PL –target 0,1,2,3,4,5,6,7 –file my.vcf

DESCRIPTION

General population genetic statistics for each SNP

OPTIONS

  Calculates basic population statistics at bi-allelic sites. The allele frequency is the number of non-reference alleles divided by the total number of alleles.  The expected hetrozygosity is 2*p*q, where p is the non-reference allele frequency and q is 1-p.  The observed heterozgosity is the fraction of 0/1 genotypes out of all genotypes.  The inbreeding coefficient, Fis, is the relative heterozygosity of each individual vs. compared to the target group.

Output : 9 columns :
     1. seqid
     2. position
     3. target allele frequency
     4. expected heterozygosity
     5. observed heterozygosity
     6. number of hets
     7. number of homozygous ref
     8. number of homozygous alt
     9. target Fis
required: t,target     -- a zero based comma separated list of target individuals corresponding to VCF columns
required: f,file       -- proper formatted VCF
required, y,type       -- genotype likelihood format; genotype : GL,PL,GP
optional, r,region     -- a tabix compliant region : chr1:1-1000 or chr1

Type: statistics

EXIT VALUES

	0		Success
	not 0		Failure

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.