How to convert PLINK file (map, ped) to haplotype file for XPEHH application

Question

[Victor]

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

Answer 1

[Wietje]

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...