Question: Cutting up plink .ped/fam files to create files for n genomic windows
0
gravatar for seanstankowski
16 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 • 592 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 16 months ago by seanstankowski0

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

ADD REPLYlink written 16 months ago by seanstankowski0
2
gravatar for chrchang523
16 months ago by
chrchang5233.5k
United States
chrchang5233.5k 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 16 months ago • written 16 months ago by chrchang5233.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1510 users visited in the last hour