Rerun type 1 does not work as expected

Kennedy-Lab-UW / Duplex-Seq-Pipeline

A standalone end-to-end data analysis pipeline for Duplex Sequencing

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Rerun type 1 does not work as expected #94

Closed bkohrn closed 3 years ago

bkohrn commented 3 years ago

Rerun type 1 repeats the variant caller, but does not redo clipping. This is in contrast to the README, which says:

Issue Amount to rerun rerun_type

Wrong target bed file used
Wrong clipping parameters used
From pre-variant calling 1

Issue	Amount to rerun	rerun_type
Wrong target bed file used Wrong clipping parameters used	From pre-variant calling	1

bkohrn commented 3 years ago

Proposed solution: Previously (in v1.X.X), there was a pre-variant calling checkpoint. This was removed in v2.0.0 (don't quite remember why). I could re-add it as a post-BLAST processing step and modify the rerun script to reset to that script.