I think I have a fairly simple question but my search engine efforts have been unsuccessful.
I recently started working with plink (v1.9) and I'm using it to get a correlation matrix between a list of SNPs. The command I use is:
plink --bfile <relevant bfile> --extract <txt document with list of snps> --r square gz --write-snplist --out <output>
Assume that my SNP text file holds the following (fake) SNPs in CHR:BP format: 1:11, 1:9, 1:13
The contents of the text file generated by
--write-snplist: 1:9, 1:11, 1:13.
I want the columns of my output to be the names of the SNPs I used. My question is: will the columns of the correlation matrix be in the order of the
--extract file or the