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Do I have to adjust contig ploidy priors with mainly male/female samples in germline CNV calling
If my cohort used for model building consists mainly of male samples do I have to use priors different from
CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_3
X 0.01 0.49 0.49 0.01
Y 0.50 0.50 0.00 0.00
for X and Y chromosomes, as the probability for having a Y is much higher than 50% in this special cohort or are these only starting parameters which are improved when the model is trained?