Can we add additional columns to ped and map files in PLINK?

Question

[Nirodha]

Hello,

I need to know whether we can add additional columns to PLINK file formats.

Specifically, I am trying to create PLINK file formats, by using my simulated data. I need to know that in a .ped file format in PLINK, can we add additional columns (ex: a column represent age of individuals) after the first six mandatory columns? I need to store additional information which is important for further studies. Also, can we do this to map files as well? (ex: In map file can we store additional details about SNPs, like selection coefficients, dominance coefficients etc.).

If these are not possible in PLINK's standard file formats do we have an option to keep these information in PLINK file format?

Thank you very much for your time.

Nirodha

Answer 1

[chrchang523]

No, you can't do this in the .ped + .map file format, which has been obsolete for close to a decade. You can with PLINK 2.0's file format; see https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 for an example where the sample-information file (.psam) has extra "Population" and "SuperPop" columns.

[Nirodha]

Thank you very much for this information.