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xpEHH
jewmanchue edited this page Jun 9, 2014
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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.
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 : zev.kronenberg@utah.edu
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.
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