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Are there any default --contig-ploidy-priors available?
I've recently been working through the tutorial for GermlineCNVCaller (https://software.broadinstitute.org/gatk/documentation/article?id=11684) so I can then apply the pipeline to my own human exome data.
In the ploidy determination step the DetermineGermlineContigPloidy tool requires --contig-ploidy-priors. Are there any default files available for this? (Particularly for hg19 data) I have found an example that has ploidy values for chr1, chr2 and chrX and chrY and I assume (a risky thing to do) that the values for chr1-2 can be extended to chr3-chr22. Naturally I'd like to be sure that is the case.
I have seen earlier posts on this topic, but they are from february so perhaps default files exist now?
(P.S = I'm only available to select category "Zoo & Garden" I don't know why, I meant to post this in the GATK support forum)