Defining Sex Chromosomes in PLINK for a Camel Genome

Question

[Smilesky]

I am analyzing whole-genome variant data from a camel species which has 36 autosomes. Since PLINK only accepts numerical chromosome identifiers, I have assigned chromosome X as 37 and chromosome Y as 38.

From this below command:

plink --vcf Chromosomes.vcf --make-bed --chr-set 38 --out plink_data 

Will plink automatically understand that 37 is Chromosome X and 38 is Chromosome Y? Or is there any additional parameter that i should mention?

Answer 1

[chrchang523]

From the --chr-set documentation:

"--chr-set changes the chromosome set. The first parameter specifies the number of diploid autosome pairs if positive, or haploid chromosomes if negative. (Polyploid and aneuploid data are not supported, and there is currently no special handling of sex or mitochondrial chromosomes in all-haploid chromosome sets.)

Given diploid autosomes, the remaining modifiers let you indicate the absence of specific non-autosomal chromosomes, as an extra sanity check on the input data. Note that, when there are n autosome pairs, the X chromosome is assigned numeric code n+1, Y is n+2, XY (pseudo-autosomal region of X) is n+3, and MT (mitochondria) is n+4."

Thus, --chr-set 36 is what you're looking for, not --chr-set 38.