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broadinstitute / lrma-aou1-panel-creation

Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.
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Investigate vcfdist behavior when evaluating inconsistent haplotypes. #19

Open samuelklee opened 1 month ago

samuelklee commented 1 month ago

Post-Shapeit4 vcfdist metrics looked good despite remaining issues with overlapping alleles, suggesting that perhaps vcfdist may not be sensitive to this (or at least not when running in its default mode). In fact, I wonder if the partial credit vcfdist essentially assigns may be misleading. Should just require running a few toy examples to verify behavior.

samuelklee commented 1 month ago

Perhaps also explore impact of --largest-variant 5000 default.