Plink v1.9: Order of SNPs when extracting from file
1
0
Entering edit mode
11 days ago
docj • 0

Hello everyone.

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 --write-snplist file?

Thank you.

plink • 158 views
ADD COMMENT
1
Entering edit mode
11 days ago

Practically all plink output commands (including both --write-snplist and --r) are based on the variant order in the input .bim file.

ADD COMMENT

Login before adding your answer.

Traffic: 1311 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6