Running genome-wide selection studies, one usually needs to convert the data set obtained by phasing program, e.g., BEAGLE, into input file to count different statistics to get the signals of selections. One of such test is based on extended haplotype homozygosity (EHH). To perform it, I recommend an R package REHH2.0. Below is the script I wrote to convert output files produced by BEAGLE into input files for REHH2.0.
Dear Gennady, thank you very much for sharing this script !
I have .vcf files with phased genotypes, produced with Beagle. I was wondering how to convert them to .hap format. Do you have any suggestion? Or are you aware of a tool that can do it?
Best regards, Lucas
Dear Lucas!
Thank you for your comment. As I noticed, REHH2.0 package consumes inp/hap files of its own format. I wasn't lucky with the searching of tools to make inputs for this package. I turned to write custom scripts. Feel free to send me an example of your vcf file and I will write a script to convert it to REHH2.0 inputs.