VS-695. Updates to run Precision and Sensitivity on VQSR Lite #8230
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… scale of calibration_sensitivity vs. lod score. Also retrieving score from JointVcfFiltering and storing that in BQ and in the VCF. Probably don't need this long term.
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8230 +/- ##
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Coverage ? 85.837%
Complexity ? 35510
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Files ? 2194
Lines ? 167039
Branches ? 18004
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Hits ? 143382
Misses ? 17269
Partials ? 6388 |
RoriCremer
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Mar 3, 2023
src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortLite.java
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RoriCremer
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| @@ -247,6 +248,12 @@ protected String[] customCommandLineValidation() { | |||
| errors.add("Parameters 'project-id', 'dataset-id', 'call-set-identifier', 'wdl-step', 'wdl-call', and 'shardIdentifier' must be set if 'cost-observability-tablename' is set."); | |||
| } | |||
| } | |||
| if (truthSensitivitySNPThreshold < 0.0 || truthSensitivitySNPThreshold > 1.0) { | |||
| errors.add("Parameter 'snps-truth-sensitivity-filter-level' MUST be between 0.0 and 1.0'"); | |||
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should we print out what the number actually is?
RoriCremer
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RoriCremer
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src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/CreateFilteringFiles.java
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This was referenced Mar 17, 2023
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Update GvsCalculatePrecisionAndSensitivity.wdl to allow for different scale of calibration_sensitivity vs. lod score.
Also retrieving score from JointVcfFiltering and storing that in BQ and in the VCF. (Probably don't need this long term.)