Question: Reorder samples in a PLINK dataset
0
gravatar for pufferfish
5.8 years ago by
pufferfish260
South Africa
pufferfish260 wrote:

Is it possible to reorder samples in a PLINK dataset, per an order specified in a second file

I've tried the "--keep" and "--recode" options, but they don't do it

plink • 4.8k views
ADD COMMENTlink modified 5.8 years ago by chrchang5236.6k • written 5.8 years ago by pufferfish260

Interesting to know why would you need them to be ordered?

ADD REPLYlink written 5.8 years ago by zx87549.1k
1

Some programs like PREST-plus need the data to be sorted by FID/IID to run properly.

ADD REPLYlink written 4.3 years ago by nalliey.bsd10
7
gravatar for chrchang523
5.8 years ago by
chrchang5236.6k
United States
chrchang5236.6k wrote:

plink --bfile [original fileset] --indiv-sort f [file describing new order] --make-bed --out [new prefix]

(More discussion at https://www.cog-genomics.org/plink2/data#indiv_sort .)

ADD COMMENTlink written 5.8 years ago by chrchang5236.6k

ah.. plink2!

ADD REPLYlink written 5.8 years ago by pufferfish260
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