xpEHH - zeeev/vcflib GitHub Wiki

Description

XPEHH is a popular tool for examining the differences in haplotype decay between two populations. For further reading follow the link: [Sabeti et al. 2007(http://www.nature.com/nature/journal/v449/n7164/full/nature06250.html). The standard implementation of XPEHH requires phased and imputed genotypes.

Usage statement for xpEHH:

INFO: help
INFO: description:
     xpEHH estimates haplotype decay between the target and background populations.  Haplotypes are integrated
     until EHH in the target and background is less than 0.05. The score is the itegrated EHH (target) / integrated EHH (background).
     xpEHH does NOT integrate over genetic distance, as genetic maps are not availible for most non-model organisms.
Output : 4 columns :
     1. seqid
     2. position
     3. alllele frequency
     4. EHH-alt
     5. EHH-ref
     6. xpEHH

INFO: xpEHH  --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf

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

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

Running xpEHH with provided data:

cd samples 
bgzip scaffold612.vcf
tabix -p vcf scaffold612.vcf.gz

bin/xpEHH --target  1,20,25,29,30,38,43,46  --background \
2,3,4,5,6,7,21,22,22,23,24,26,26,28,31,32,33,34,35,36,37,39,40,41,42,44,45 \
--file samples/scaffold612.phased.vcf --type GP > t.txt

 R --vanilla < bin/plotXPEHH.R --args t.txt 

The resulting plot:

While this plot does not look as impressive as the associations tools' output (pFst, wcFst & pFst) it reflects reality.