Opened 10 months ago

Closed 10 months ago

#1563 closed defect (fixed)

The Bwa-Mem alignment step should not disable genotype qc

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.52.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

When the Bwa-mem alignment step was implemented in #1473, the genotype qc wizard didn't support checking WGS data, so the QC_GenoTypeStatus annotation was set to Disabled. Support for WGS data in the qc wizard was implemented later (in #1483 and #1487), but since all WGS data had already been aligned, we forgot to remove the code that disable the qc check.

This code should be removed. Existing alignments should be fixed manually (eg. clear the QC_GenoTypeStatus annotation).

Change History (1)

comment:1 by Nicklas Nordborg, 10 months ago

Resolution: → fixed
Status: new → closed

In 7562:

Fixes #1563: The Bwa-Mem alignment step should not disable genotype qc

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