popStats(1) · carta

Usage

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

General population genetic statistics for each SNP

: 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

3 releases since Debian 11 (Bullseye); the text changed 2 times.