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confirming my analysis strategy to work with sex chromosomes
So, I wanted to confirm/discuss as I need to deal with sex chromosomes in my project. I have come across this post: https://gatkforums.broadinstitute.org/gatk/discussion/4639/x-chromosome-gentyping, but I wanted to be sure as the pipeline changed since 2014.
I am working on a non-human mammal which has reference genome from a female (so only X chromosome present for mapping). I have 81 samples out of which I have a mix of male and female samples.
For the first run, when I was not so much concerned about sex chromosomes, I ran everything (autosomes and sex chromosomes) using the default method (diploid for all samples and chromosomes). For female samples, it is fine. (Correct me if I am wrong). Since there are two copies of the X chromosomes, they are diploid for a variant call.
For male samples, I run them with ploidy =1 in haplotypecaller (gvcf), as males have just one X chromosome? What about them in genomicsDBimport and GeontypeGVCF?