treat chrX as autosome

[Samuel Hollinger]

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. This happens even when I specify "--allow-extra-chr". "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 PLINK1.9, 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.

[Christopher Chang]

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.