How to process Plink2 --score across chromosomes

Question

[Travis]

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.

Answer 1

[chrchang523]

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