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
1 answer
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...
Log in to answer this question.
-
selscan XPEHH map file
written by SeoG •
-
PLINK ped file
written by loy_loy •
-
PLINK error message
written by lovegenetics •
-
how to deal with 0 in allele from ped/map files
written by Victor •
-
the XP-EHH instruction
written by Victor •
-
Convert GBS hapmap file into Plink bed file
written by hd59430 •
-
Dealing with half missing calls in ".ped" file
written by reza.jabal
-
Subset loci by chromosome in plink
written by thegreasyskillet •
-
Plink or vcf 1000 genomes files with INDEL format I/D
written by 1888
-
How To Prepare The Input For The Germline Software For The Inference Of Ibd Patterns
written by Tim •
