--chr-set PLINK
0
0
Entering edit mode
2.8 years ago
Matteo ▴ 10

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!!

sex plink chromosomes mitochondrial --chr-set autosomes • 2.4k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1562 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6