Now that GATK supports ploidy, how do people generate ChrX calls. My first guess is to have 2 separate genotyping runs, one for males with ploidy=1 and a second for females only with ploidy=2?
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Now that GATK supports ploidy, how do people generate ChrX calls. My first guess is to have 2 separate genotyping runs, one for males with ploidy=1 and a second for females only with ploidy=2?