Opened 5 months ago

Closed 5 months ago

#1557 closed enhancement (fixed)

Add support for setting the "f-score-beta" parameter when filtering WGS variant calls

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.51
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The default value of 1.0 optimizes the precision and sensitivity, but it would be nice to be able to adjust this parameter. The selected value should be saved as an annotation, and it may also be nice to import the resulting "threshold" value from the filter-stats file afterwards.

Change History (6)

comment:1 by Nicklas Nordborg, 5 months ago

In 7504:

References #1557: Add support for setting the "f-score-beta" parameter when filtering WGS variant calls

Added new annotation types: F_SCORE_BETA and VariantsFilterThreshold

comment:2 by Nicklas Nordborg, 5 months ago

In 7505:

References #1557: Add support for setting the "f-score-beta" parameter when filtering WGS variant calls

The "threshold" value is imported from the filtering-stats.txt file.

comment:3 by Nicklas Nordborg, 5 months ago

In 7506:

References #1557: Add support for setting the "f-score-beta" parameter when filtering WGS variant calls

The job script generator now supports setting the f-score-beta parameter.

comment:4 by Nicklas Nordborg, 5 months ago

In 7507:

References #1557: Add support for setting the "f-score-beta" parameter when filtering WGS variant calls

Added a field for setting the F-score beta parameter when starting the variant calling.

comment:5 by Nicklas Nordborg, 5 months ago

In 7508:

References #1557: Add support for setting the "f-score-beta" parameter when filtering WGS variant calls

Added the new annotation to the release export.

comment:6 by Nicklas Nordborg, 5 months ago

Resolution: → fixed
Status: new → closed
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