Fix for PossibleDeNovo annotation to work without Genotype Likelihoods #7662
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ldgauthier
approved these changes
Feb 8, 2022
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PossibleDeNovo checks each trio's genotype (including parent hom ref genotypes) for likelihoods even though it doesn't actually use the PLs. The PLs can get dropped if GVCFs are reblocked which means this annotation no longer works as expected. This changes the check to look for GQs instead of PLs as the GQs are used as part of the annotation.
@ldgauthier Could you please suggest a reviewer?