Question: How to convert PLINK file (map, ped) to haplotype file for XPEHH application
1
gravatar for Victor
16 months ago by
Victor10
Australia
Victor10 wrote:

Hello

I am the first year PhD student in University .

Basically, I'm new to PLINK (obviously). Sorry for asking quite a silly question.

I am doing the selection signal with canine and try to use the HP-EXX (https://github.com/joepickrell/xpehh) to get the haplotype score.

However, I only have Plink files (ped, map). I want to know are there any way to convert my plink files to haplotype format. The software require the input haplotype format is one haplotype per line, with alleles coded as 1 and 0.

Many Thanks

snp genome • 752 views
ADD COMMENTlink modified 16 months ago by Wietje210 • written 16 months ago by Victor10
2
gravatar for Wietje
16 months ago by
Wietje210
Germany
Wietje210 wrote:

To define haplotypes you will need to phase your data (e.g. with Beagle or Shapeit); the conversion to 0-1 format can be accomplished in PLINK (--recode 01). you might want to take a closer look at the PLINK manual and the various options.

And maybe check whether your question has popped up before...

ADD COMMENTlink written 16 months ago by Wietje210
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