Basic population statistics with GPAT

To generate simple statistics about a population use the popStats tool.

INFO: help
INFO: description:
      General population genetic statistics for each SNP

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
INFO: usage:  popStat --target 0,1,2,3,4,5,6,7 --file my.vcf

INFO: required: t,target     -- a zero based comma seperated list of target individuals corrisponding to VCF columns
INFO: required: f,file       -- proper formatted VCF
INFO: required, y,type       -- genotype likelihood format; genotype : GL,PL,GP
INFO: optional, r,region     -- a tabix compliant region : chr1:1-1000 or chr1
INFO: version 1.0.0 ; date: April 2014 ; author: Zev Kronenberg; email : zev.kronenberg@utah.edu

example with distributed data:

bin/popStats --target 0,1,2,3,4,5,6,7 --file samples/scaffold612.vcf --type PL > \
scaffold612.target.stats.txt