--chr-set PLINK

Question

[Matteo]

Hi,

I've got .bed/.bim/.fam SNP file of an organism with 44 autosomes. I have renamed the sex chromosomes 45 and 46, and the mitochondrial 47. How should I specify --chr-set in PLINK? The first parameter represents the number of autosomes (N), so it should be 44. I understand that PLINK automatically assumes N+1 and N+2 are the sex chromosomes. But how do I specify the mitochondrial? In my case that is N+3, but PLINK considers N+3 to be the pseudo-autosomal region of X.

Thanks in advance!!

[Sam]

maybe just set MT to N + 4 and if you don't want the XY region, use no-xy? https://www.cog-genomics.org/plink/1.9/input#chr_set