Plink. Convert ped files of artificially mixed population into vcf using recode

Question

[Mr Locuace]

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.

Answer 1

[Wietje]

The options recoding options influence how the sample ID in the VCF file is composed, check the PLINK manual or this link for that:

"The 'vcf', 'vcf-fid', and 'vcf-iid' modifiers result in production of a VCFv4.2 file. 'vcf-fid' and 'vcf-iid' cause family IDs and within-family IDs respectively to be used for the sample IDs in the last header row, while 'vcf' merges both IDs and puts an underscore between them (in this case, a warning will be given if an ID already contains an underscore)."

https://www.cog-genomics.org/plink/1.9/data

The iid and fid options are mainly interesting when working with family sets - are your samples at all related? Does ancestry/ relationship play a role? Otherwise I would say you can easily go with the regular --recode vcf.

[Mr Locuace]

Thank you @Wietje !. No, the samples are not related.