Workflow to apply NCR and reference artifact filters and remove zero-carrier sites #653
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We need to have an offline discussion about how to streamline these downstream steps. Not ideal to have two implementations of NCR. |
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Updates
Create a standalone WDL for NCR and reference artifact filters. Also removes sites with zero carriers. This script pulls code from the existing NCR calculation in apply_sl_filter.py but applies it independently from genotype filtering to allow for intervening steps like outlier removal and CPX filtering which impact the NCR calculation.
Marked as draft while AoU Phase 2 downstream steps development is ongoing.