Evoquer: a BigQuery-based joint calling tool #6011
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Codecov Report
@@ Coverage Diff @@
## master #6011 +/- ##
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Coverage ? 7.002%
Complexity ? 2962
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Files ? 1998
Lines ? 150096
Branches ? 16654
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Hits ? 10509
Misses ? 138811
Partials ? 776
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I've rebased this branch and updated it to the latest |
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droazen
changed the title
Fix genotype allele remapping issue
Set samplesAreUniquified = false in ref confidence merger to avoid sample name mangling
Add a hack to skip sites with the wrong number of values in allele-specific annotations
This is necessary to work with our current test datasets
More robust hack to deal with malformed allele-specific annotations
evoquer.sh improvements
Handle missing values (".") in AS_QualByDepth
Add additional VCF header line declarations required by the GnarlyGenotyper
Avoid potential NPE in onShutdown()
Update test dataset name
Keep the NON_REF allele during merging when running the GnarlyGenotyper
Comment out empty annotations in GnarlyGenotyper
Updates to evoquer.wdl
Add clarification about removal of NON_REF allele
More evoquer.wdl updates
Support raw precomputed AVRO inputs
Add a --run-query-in-batch-mode argument
More WDL updates
Add WDLs
Set PIPELINE_MAX_ALT_COUNT to 50 in the GnarlyGenotyper to work around an IndexOutOfBoundsException
dalio run 2 WDL settings
Switch to 'evoquer_dalio40k_july_updated_dataset_map'
Replace USING with ON in the main query, and adjust WHERE clause for better query performance
GnarlyGenotyperEngine: create GenotypeLikelihoodCalculators on-the-fly when there are too many alleles
Add dalio WDL + supporting files to scripts/unsupported/evoquer
Update WDL to use clustered versions of the dalio tables
Remove old WDL directory to avoid potential confusion
Revert "Replace USING with ON in the main query, and adjust WHERE clause for better query performance"
This reverts commit 80e5140.
Switch to the latest gatk/master version of the GnarlyGenotyper
Switch back to shaded NIO classes
added optimized query
Andrea bug fix: don't reuse Avro records in Storage API
evoquer integration tests
Remove temporary seenPositions hack from the EvoquerEngine
Fix some failing tests
Fix post-rebase breakage
fix for jackson dependency issue
only update minicluster to 3+
updating to use hadoop3 everywhere
adding NO_GCE_CHECK=true
make tests cloudy
make errors more verbose
replace 2.11 with scalaVersion
Update Evoquer integration test expected output
Update to google-cloud-java 0.117.0
Don't hardcode the project ID in executeQueryWithStorageAPI()
Update protobuf-java to 3.8.0
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* fix bug in median calculation along with unit test * Parameterize table name to use for list of samples, and update query to only extract that list of samples. This adds a new capability of subsetting, but also fixes a bug where the unrestricted query extracted samples that were not in the sample_list and thus the inferred genotypes could be incorrect * Function to dry-run query in order to get the estimated bytes processed * fixed test case * revert changes for ExcessHet to match master * Disable CNNVariantPipelineTest.testTrainingReadModel until failures are resolved. (#6331) Co-authored-by: Andrea Haessly <ahaessly@broadinstitute.org> Co-authored-by: Chris Norman <cnorman@broadinstitute.org>
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