VS-1009 Add SCORE to VQSR Lite VCF #8423
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- Pull it from the VCFs exported from VQSR Lite and store it in the model
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8423 +/- ##
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Github actions tests reported job failures from actions build 5590654477
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Github actions tests reported job failures from actions build 5602967249
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rsasch
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Jul 20, 2023
src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java
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mcovarr
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Jul 24, 2023
* Add the VQSR Lite field 'SCORE' to the data model - Pull it from the VCFs exported from VQSR Lite and store it in the model * Add code to put SCORE in the extracted VCF * Pass the gatk_override to VQSRClassic wdl (oops) * Update truth for integration test to include VQSR Lite VCFs with 'SCORE' field in them * Update VQSR Lite avro file and test data to include SCORE field. * Updated dockers and override jar
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This PR adds the 'SCORE' field as an output in the VQSR-Lite derived VCFs
Score is the value from which the
CALIBRATION_SENSITIVITYis derived. The latter is what we use for filtering based on sensitivity, but Sam and Laura also want the SCORE stored in the VCF.Passing Integration test here