Question: How to process Plink2 --score across chromosomes
0
gravatar for Travis
6 months ago by
Travis10
Travis10 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 • 286 views
ADD COMMENTlink modified 6 months ago by chrchang5235.5k • written 6 months ago by Travis10
1
gravatar for chrchang523
6 months ago by
chrchang5235.5k
United States
chrchang5235.5k wrote:

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

ADD COMMENTlink written 6 months ago by chrchang5235.5k
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