Add concatenation, deduplication, and filtering to current phasing WDLs.

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.

1 stars 0 forks source link

Add concatenation, deduplication, and filtering to current phasing WDLs. #5

Closed samuelklee closed 1 month ago

samuelklee commented 1 month ago

To support #1. Depends on #2. I currently take the HiPhase output from a run of the existing phasing pipeline, do short+SV concatenation+deduplication+MAC filtering in a notebook (since only concatenation+MAC filtering is done by the existing pipeline), and then run the result through a Shapeit4-only pipeline. This should just be a quick modification of the existing WDLs.