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

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2025 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.