I wonder whether it exists an easy way to conserve haplotypes when proceeding some basic actions with plink. Is there any options? I couldn't find on my own.
The situation is as following: we have phased data. We use the .ped and .map format. We want to apply some filters (e.g keep SNPs with Minor allele frequency above 5% in our set of individuals, keep a subset of individuals, etc.). But we figured out that plink do not keep the phased in this case. Everything is mixed up in the output files.
Thanks for the support! Regards Pierre