How to generate text file having SNP list from bim file in plink?

Question

[amitgourav.ghosh12]

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?

Answer 1

[Vivek]

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.

[amitgourav.ghosh12]

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.

[amitgourav.ghosh12]

Thank you very much again! It worked.