Hi - I am working with Y chromosome data, and we have called our sequencing data with GATK 184.108.40.206 using best practices. I was not sure whether to use ploidy=1 or 2 in this case (we are working with male subjects only), so I did it both ways to compare the difference.
In our diploid results, the median depth per site is around 14, but in the haploid results (ploidy=1), the median depth per site is only around 5. Is this to be expected with haploid calls? It seems to me that the depth should be the same: calls mapped to Y are mapped to Y before we call the variants, whether we call them as diploid or haploid. Indeed, when I run chrMT, the depth is identical between the two methods; so why not also for chrY? The ONLY difference between my two methods is that I added ploidy=1 for the haploid calls in HaplotypeCaller. Any thoughts/advice/comments would be appreciated!
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