Cutting up plink .ped/fam files to create files for n genomic windows

Question

[seanstankowski]

Hi All,

There is a population genomic analysis that I want to apply to n genomic windows for large snp dataset (i.e., 10 kb windows). The analysis package reads plink .ped/.fam files or plink binary files.

Is there a way in plink to export n .plink/.ped datafiles for a given window size or even a window of n snp's?

Alternatively, what would a basic approach for generating these files look like in unix or python?

Thanks in advance

Sean

[seanstankowski]

Thanks for the fast response. I think I can manage that!

Answer 1

[chrchang523]

You can use a bash for loop which repeatedly makes plink calls of the form "plink --bfile ... --chr ... --from-kb ... --to-kb ... --make-bed --out ..."