Question: How to generate text file having SNP list from bim file in plink?
0
gravatar for amitgourav.ghosh12
3 months 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 • 158 views
ADD COMMENTlink modified 3 months ago by Vivek2.1k • written 3 months ago by amitgourav.ghosh1230
1
gravatar for Vivek
3 months ago by
Vivek2.1k
Denmark
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 3 months 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 3 months ago by amitgourav.ghosh1230

Thank you very much again! It worked.

ADD REPLYlink written 3 months ago by amitgourav.ghosh1230
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