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CombineGVCFs / GenotypeGVCFs and ploidy
I am setting up a pipeline for HaplotypeCaller and there is something I do not understand. In the manual pages of CombineGVCFs and GenotypeGVCFs it is said: "This tool is able to handle any ploidy (or mix of ploidies) intelligently; there is no need to specify ploidy for non-diploid organisms".
But then there is the description of the "--sample_ploidy" argument. Do I have to set the number of samples?
And if I want to genotype the X chromosome for a set of samples (for which, depending on the sex, HC was run with ploidy 1 or ploidy 2), do I have to do something special?