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Dear GATK team,
when I use the UnifiedGenotyper to call variants in chrX and/or chrY with ploidy=2, does the program call the variants and genotypes in the pseudoautosomal regions PAR1 and PAR2 correctly? More specifically, does the UG acknowledge that these regions are homologous on the X and Y chromosome, even though they differ in chromosomal position? If the UG does not take care of this by default, is there a way I can handle this? I read point 6 of this page, but I could not find the answer there: