Question: Cutting up plink .ped/fam files to create files for n genomic windows
0
gravatar for seanstankowski
7 months ago by
seanstankowski0 wrote:

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

plink sequence genome • 363 views
ADD COMMENTlink modified 7 days ago by Biostar ♦♦ 20 • written 7 months ago by seanstankowski0

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

ADD REPLYlink written 7 months ago by seanstankowski0
2
gravatar for chrchang523
7 months ago by
chrchang5232.6k
United States
chrchang5232.6k wrote:

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 ..."

ADD COMMENTlink modified 7 months ago • written 7 months ago by chrchang5232.6k
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