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broadinstitute / tgg_methods

Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
MIT License
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PloidyConflict & Comprehensive Ploidy Investigation #89

Open matren395 opened 3 months ago

matren395 commented 3 months ago

One major curiosity about the new DRAGEN callset is the fact that it imputes the biological sex of samples and makes their sex chromosome calls haploid as appropriate, or marks them with a 'PloidyConflict' flag as appropriate. However, we 1) do not see this 'PloidyConflict' flag in the delivered callset and 2) do not know quite as much as we'd like about how these imputations are performed 3) aren't returned the (apparently existing) output metrics for these. This ticket exists for the investigation of all three of these, as it relates to sex and ploidy and imputation in the newly delivered callset.

matren395 commented 3 months ago

Some further discussion has found that , once we CONFIRM that where we should be seeing 'PloidyConflict' flags in the FT field are there in the DRAGEN gVCFs , can can load the data as-is. We don't have to set XX-individual diploid variants in ChrY as NA or any fixes like that. Still we want to confirm WHY we are seeing these.

matren395 commented 1 week ago

This is on hold... this was not delivered with the gVCFs or single-sample VCFs , and we can't find it anywhere in the DRAGEN pipeline. We were able to appropriately run sex & relatedness checks based off of the reported sex (seqr) and predicted sex (observed ploid), but resolving this behavior is pending...