I am trying to get the XP-EHH values by using HP-EXX. (https://github.com/joepickrell/xpehh) .
I only have map and ped plink files in two populations.
1. I used plink function --recode vcf, to make vcf files (preQC had been done, plus --snp-only -just acgt).
2. Eeagle was applied to phase my dataset. (it should have no-missing data in my output files, and all alleles become 0 and 1 only)
3 Then I wrote a R-script to format a map files for XP-EHH.
I have some questions about XP-EHH.
1. How many map file I should make for XP-EHH command?
The example ./xpehh -m example.ihsmap.................
But I have 2 populations. Should I merge the 2 map files into one? Or I should use the overlap snp?
Why I ask this it is because I try to use the big map file merged from 2 map files and always get the error message
like:"borken the pipeline or out of range........"
2. I check the ihshap file.I saw no row name or column name in the files.
I am wondering how do the script process the files. The output of example shown the chr ID. Sould I make the same order for ihsmap and ihshap?
Are there anyone has experience in process XP-EHH
Thank you for your time!!