Change SNP ID strings in PLINK files
0
0
Entering edit mode
2.9 years ago
L_to_the_m ▴ 10

Hi, I have PLINK files with SNP IDs like this:

AX-14233402__rs35404821
AX-37499887__rs74704183
AX-36783275__rs11997571

I would like to change the SNP IDs to have only the IDs without the AX-... term: rs35404821 rs74704183 rs74704183

For the .pvar file it wouldn't be a problem, but then I also need to change it within the .pgen file. Is there any solution for this? For the .pvar file it would be:

awk '{$3=A[split($3,A,"_")]}1' datafile.pvar > datafile_ID.pvar
PLINK SNP ID • 750 views
ADD COMMENT
0
Entering edit mode

Don't think the SNP ID is stored within the pgen file, so you should be good to go after modifying the pvar

ADD REPLY

Login before adding your answer.

Traffic: 1236 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6