Plink: Retrieving specific SNP data for individuals in dataset

Question

[hessjl]

I am new to plink and have a (hopefully) simple data management operation, but little idea of how to implement it. The essentials are listed here:

1. I have three genotype call files: data.bed, data.fam, and data.bim.
2. I created a file snps.txt containing a list of markers.
3. My goal is to create a file with subject IDs listed in rows and SNP IDs (as per snps.txt) as column headers with genotypes listed underneath.

Question: How might I go about performing this task?

Answer 1

[chrchang523]

If you're fine with the main body of the file containing allele counts (0/1/2) rather than allele names, you can use

plink --bfile data --extract snps.txt --recodeA

and then use Unix cut to remove any header columns you don't want.

Otherwise,

plink --bfile data --extract snps.txt --recode compound-genotypes

(this requires PLINK 1.9) will almost get you there, but you'll need to add a header line on your own. Or

plink --bfile data --extract snps.txt --recode

works if you want two columns per SNP.

[hessjl]

Thank you for the clear explanation chrchang523! The last command you provided worked like a charm.