Haplotypecaller --sample-sex

When I was doing the haplotypecaller module, I found that there is an extra parameter -sample-sex, what is the specific role of this parameter? Will the ploidy parameter for the sex chromosomes (X and Y) be set to 1 because the sample is male? Or how do I specifically set the chromosome (X and Y) -ploidy parameter to 1 for male individuals?

Hello @870281997,

I believe you can use the --range-male and --range-female to achieve this. See the documentation here:

Ploidy levels are independent to the presence of sex-chromosomes or even sex-determination. Ploidy levels correspond to the number of chromosome sets present in a somatic cell (2x:diploid, 3x:triploid, 4x:tetraploid). The ploidy level of humans is 2x (diploid), the ploidy level of bread wheat is 6x (hexaploid). Setting this parameter for the X or Y chromosome makes no sense.

TLDR: Most human somatic samples are diploid.

Best regards,