iHS - zeeev/vcflib GitHub Wiki

IHS is a popular within population test for selection. It measures the decay of haplotypes containing the reference and non-reference allele.

Usage statement for iHS

INFO: help
INFO: description:
     iHS calculates the integrated ratio of haplotype decay between the reference and non-reference allele.
     This implementation of iHS integrates over a SNP index, NOT a physical distance or genetic distance.

Output : 4 columns :
     1. seqid
     2. position
     3. target allele frequency
     4. integrated EHH (alternative)
     5. integrated EHH (reference)
     6. iHS log(iEHHalt/iEHHref)

INFO: iHS  --target 0,1,2,3,4,5,6,7 --file my.phased.vcf  --region chr1:1-1000

INFO: required: t,target  -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns
INFO: required: f,file    -- argument: proper formatted and phased VCF.
INFO: required: y,type    -- argument: genotype likelihood format: PL,GL,GP
INFO: optional: r,region  -- argument: a tabix compliant genomic range : "seqid:start-end" or "seqid"

INFO: version 1.1.0 ; date: April 2014 ; author: Zev Kronenberg; email : [email protected]