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Are there any default --contig-ploidy-priors available?

Matthieu_MMatthieu_M Santiago, ChileMember

Hello team,

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)


  • sleeslee Member, Broadie, Dev ✭✭✭

    Hi @Matthieu_M,

    It's probably safe to replicate the autosomal values for chr3-chr22. Hopefully your data should be discerning enough that your results are not overly sensitive on the prior.

    Ideally, you'd have a set of representative samples for which at least the sex genotypes are known that you can use as truth data. In any case, you should first build an initial model and manually check that your called contig ploidies and sex genotypes look reasonable. If not, this might indicate that PARs and other troublesome regions are not suitably masked. If masking does not resolve the issue, only then would I try to adjust the priors to be stronger.

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