Hello, I would really apreciate to have some feedback to a problem. I am using Plink 1.9.
I would like to get phased genotypes from an artificially mixed human population.
I merged two populations from different sources using Plink (--merge), creating pop_A. I checked whether there were no problems with the strands and make sure to have the same SNPs in both populations, in addition to performing other controls. Then, I split pop_A into 22 ped/map files.
The phasing is done with Beagle, which requires vcf files, one per chromosome. For that, I converted the 22 ped/map files to vcf format using --recode vcf. However, in some websites it is recommended to use --recode vcf-iid instead, but I don't understand the difference between these commands. So my first question is: which of these commands should I use and why.
Now the second question. Since the two original populations come from different sources (POPRES and 1000 Genomes), is it OK to convert pop_A plink files to vcf just using --recode vcf(or vcf-iid), or should I consider other issues as well?
Thank you very much in advance.