Subjects and SNPs

Question

[hi.there]

Hello,

I am trying to go from a .bim, .bed, .fam files along with a snp.txt file with rsids and their end chromosome position to a simple configuration with subjects as rows and SNPs as columns. I am not used to data manipulation in plink. I found a post which mentioned this:

Plink: Retrieving specific SNP data for individuals in dataset

.... which generated a .ped and a .map file which I do not believe is the correct format. This seems very easy but I couldn't find it in the data manipulation plink page. Would anybody know? Thank you.

Answer 1

[LChart]

which generated a .ped and a .map file which I do not believe is the correct format

The .ped format indeed has subjects as rows, and SNPs as columns. It has some extra columns providing subject and family information; and genotypes follow that information (see https://www.cog-genomics.org/plink/1.9/formats#ped). Note that the ped file contains two columns for each SNP, i.e. rsXXXX-allele1 and rsXXXX-allele2. Were you looking for genotypes encoded as 0/1/2 -- you can use --recodeA in this case.

[hi.there]

Thank you so much.