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GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #8741

Merged
merged 1 commit into from
Apr 10, 2024
Merged

GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #8741

merged 1 commit into from
Apr 10, 2024

Commits on Apr 8, 2024

  1. Several GQ0 cleanup changes: 

    Set GGVCFs --all-sites GQ0 hom-refs to no-calls
Set regular GGVCFs GQ0 hom-refs to no-calls (any DP, PL) for better AF/AN annotations
Remove PLs in "no data" case where DP=0 for more accurate QUAL score
    @ldgauthier
    ldgauthier committed Apr 8, 2024
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