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jewmanchue edited this page Jun 10, 2014
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IHS is a popular within population test for selection. It measures the decay of haplotypes containing the reference and non-reference allele.
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 : zev.kronenberg@utah.edu
Installing GPAT++ / updating:
SNP methods:
pFst, wcFst, bFst
Basic population statistics
ABBA-BABA test
Haplotype methods:
Haplotype plotting
Linkage disequilibrium
Nucleotide diversity
xpEHH
iHS
hapLrt
Utilities:
Smoothing GPAT++ output
1KG target and background index
Permutation