Question: How to process Plink2 --score across chromosomes
0
gravatar for Travis
7 days ago by
Travis0
Travis0 wrote:

I'd like to run the --score flag across chromosomes. I tried this syntax:

# PBS -t 1-22

plink2

--pfile data.chr${PBS_ARRAYID}

--score snps_file header list-variants

--memory 4500

--threads 5

This generated only one set of output files (.sscore, sscore.vars, and .log), ostensibly from chr22. I've been able to iterate this way using --clump and I wonder if I can produce either of the following: 1. Separate --score reports per chromosome or 2. One final combined report for chr's 1-22? Thanks.

plink2 • 68 views
ADD COMMENTlink modified 7 days ago by chrchang5234.6k • written 7 days ago by Travis0
1
gravatar for chrchang523
7 days ago by
chrchang5234.6k
United States
chrchang5234.6k wrote:

You can use —out to make your per-chromosome runs write to different output files.

ADD COMMENTlink written 7 days ago by chrchang5234.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2055 users visited in the last hour