Question: Is It Possible To Subset Dosage Data With Plink?
2
gravatar for chancerh
5.5 years ago by
chancerh20
chancerh20 wrote:

Hello,

I am trying to use PLINK (v1.07) to input dosage data and output a subset of that data without analyzing it. That is, I want to keep all of the SNPs but only a subset of the samples. Is this possible with PLINK? I have been using the --dosage and --write-dosage options, but I have not had any success. Details Below.

I have imputed dosage data for 5 samples in a file called test.dose that looks like this:

SNP A1 A2    F1 D1-40 F2 D2-32 F3 D3-30 F4 D4-49 F5 D5-30
7:16719 A B 1.99800005159341 1.99599998397753 1.99800005159341 1.99800005159341 1.99599998397753
7:31273 A B 1.55099993944168 1.92400002479553 1.91199994832277 1.9119999781251 1.94999995082617
...

I have a test.fam file that looks like this:

F1 D1-40 -9 -9 2 -9
F2 D2-32 -9 -9 2 -9
F3 D3-30 -9 -9 2 -9
F4 D4-49 -9 -9 2 -9
F5 D5-30 -9 -9 2 -9

I have a list.txt file that contains the following:

F2 D2-32
F5 D5-30

I am running the following PLINK command:

plink --dosage test.dose format=1 --fam test.fam --keep list.txt --noweb --write-dosage --out subset

This outputs a file called subset.out.dosage, but it doesn't contain the dosages. It looks like this:

SNP A1 A2
7:16719 A B
7:31273 A B
...

What I would like is the above file but with dosages for the samples contained in list.txt. I realize that there are many tools for manipulating text, but is this possible with PLINK?

plink • 2.6k views
ADD COMMENTlink written 5.5 years ago by chancerh20

Didn't test it, but GenGen might do it, see combine_snptest.pl file1 -keep caseid.keep -prefix caseonly. Why do you need to subset?

ADD REPLYlink written 5.5 years ago by zx87546.8k
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