Force PLINK2 to neglect chrX as the sex chromosome

Question

[8armed]

I'd like to run PLINK2 on a vcf file to do linkage pruning, followed by a PCA. The input vcf file is from a non-human organism. I have already excluded the known sex chromosome from the vcf file. However, when I run PLINK2, I always get an error since it recognizes chrX as the sex chromosome. How can I force PLINK2 to treat chrX as a normal autosome (which is the case in my species). PLINK2 makes a few suggestions for how one may solve the error (see below the error message), but I don't find any of those solutions straight forward to simply force PLINK2 to not treat chrX as the sex chromosome. Notably, when I instead run PLINK (and not PLINK2), I don't get a respective error.

Here the command I run for linkage pruning:

plink2 \
--vcf ${FILE}.vcf \
--allow-extra-chr \
--set-all-var-ids @:# \
--indep-pairwise 50 10 0.3 \
--make-bed \
--out ${FILE}_pruningFact.0.3 

Here the error I'm getting:

Error: chrX is present in the input file, but no sex information was provided;
rerun this import with --psam or --update-sex.  --split-par may also be
appropriate.

Answer 1

[chrchang523]

(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII )

You need to use --chr-set, not --allow-extra-chr, to specify a nonhuman chromosome set.

Your command line was just as wrong for PLINK 1.9 as it was for PLINK 2.0, but PLINK 2.0 has better sanity-checking.