Dear all,

I am interested in exploring the H12 analysis to detect putative markers under selection using haplotype information. The approach fairly simple and is described in detail in Garud et al (2015). My question is: how can I get my vcf/ped/bed/ files into proper format?

According to the SelectionHapStats documentation in Github, the input file is a line-by-line listing of all the coordinates on the chromosome where there is a polymorphism and the nucleotide states in each individual in the sample

The input file should look something like this:

3948,A,A,A,N,T,A,A,A,T,…etc
7387,A,N,G,G,G,G,G,A,G,…etc
19921,T,G,T,T,T,G,G,T,G,T,…etc
etc..

Using --recode and --transpose flags in plink gives me a similar format, but not quite the same. Any ideas?

Thanks for your help