Question: How to generate text file having SNP list from bim file in plink?
gravatar for amitgourav.ghosh12
25 days ago by
amitgourav.ghosh1230 wrote:

I have generated a bim file having about 24 million SNPs, how do I make a text file from it containing only the SNP names list so that I can use it to extract sample data from data set in fam format?

snp • 93 views
ADD COMMENTlink modified 25 days ago by Vivek2.1k • written 25 days ago by amitgourav.ghosh1230
gravatar for Vivek
25 days ago by
Vivek2.1k wrote:
awk '{print $2}' your_file.bim > snplist.txt

Would work to give you a SNP list but I don't clearly understand what you are trying to do after that. If you are looking to subset a dataset for individuals you need to specify the individuals you want to keep/remove to PLINK.

ADD COMMENTlink written 25 days ago by Vivek2.1k

Thank you very much for your answer. I shall try it out, I am novice in this field, trying to filter out individuals in a data set using plink having all the 24 million SNPs. These set of SNPs were found out to be present in both data sets in my study.

ADD REPLYlink written 25 days ago by amitgourav.ghosh1230

Thank you very much again! It worked.

ADD REPLYlink written 24 days ago by amitgourav.ghosh1230
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1553 users visited in the last hour