Reviewed pipelines with dev team.
HSP updates:
- Calling SNPs and Indels at the same time then using SelectVariants to separate them for filtering
- Moved logs next to the files like in WGP
- Flattened outputs into one directory
- The file names for the final outputs are now <projectName>.vcf and <projectName>.eval
- Updated test to pass the chr20 intervals instead of a boolean
- Removed MultiFCP
WGP updates:
- Only cleaning and calling chromosomes 1-22, X, Y, MT
- Splitting SNPs from indels, filtering indels, then merging the selected SNPs and selected Indels back together to make sure there are no collisions in CombineVariants
- Still running VQSR on the recombined SNPs plus hard filtered indels
- Using hard indel filters from delangel
- Reduced number of tranches with rpoplin
- Changed prior for dbsnp from 10 to 8 with rpoplin
- Assuming identical samples on both CombineVariants
- Explicitly using variant merge option UNION even though it's the default
- Not setting the default genotype merge option PRIORITIZE
- Generating a vcf and eval for each tranche
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5825 348d0f76-0448-11de-a6fe-93d51630548a
Minor updates to the FCPTest to match the changes due to using the old indel caller.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5766 348d0f76-0448-11de-a6fe-93d51630548a
Feeding FCP UG the bam list instead of individual bams to cut scatter gather time from O(m^100) as measured by Chris to O(m^1).
Fixed NPE when eval values aren't found in PipelineTests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5694 348d0f76-0448-11de-a6fe-93d51630548a
Added a rudimentary GATKReportParser for parsing VE3 results.
Re-enabled the FCPTest using VE3, the GATKRP, and the PicardAggregationUtils.
The tag type for .rod files is DBSNP, not ROD.
More explicit return types on implicit methods.
Added null checks for implicit string to/from file conversions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5668 348d0f76-0448-11de-a6fe-93d51630548a
Switched YAML parser to new Broad parser which will additionally update picard cleaned bams to the latest version if the project and sample are specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5634 348d0f76-0448-11de-a6fe-93d51630548a
Disabled the MFCP while the FCP gets an update.
Minor updates to email messages for upcoming scala 2.9.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5588 348d0f76-0448-11de-a6fe-93d51630548a
TODO: Switch to bulk status checks and add status archive lookups.
Sending SIGTERM(15) instead of SIGKILL(9) to allow for graceful termination of child process.
Printing out the name of the QScripts in the compile error text.
Added a pipelineretry -PR pass through for the MFCP and MFCPTest.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5295 348d0f76-0448-11de-a6fe-93d51630548a
Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done.
Enabled the MCFPTest for the first time, running without the tear script.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a
Bug smashes for the MCFP:
Synchronized access to LSF library and modifications to the QGraph.
If values are missing from the graph with -run make sure to exit with a non-zero.
Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
Added jobPriority and removed jobLimitSeconds from QFunction.
All scatter gather is by default in a single sub directory queueScatterGather.
Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a
Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod.
Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info).
Renamed fCP.q to FCP.q.
Though it's still disabled until VariantEval is updated, added changes above to the FCPTest.
Removed refseq table from the queue.sh wrapper script. Only specified in the yaml.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
Updated LibBatIntegrationTest to use proper networked temp directory accessible by local machines and nodes.
Disabling the FCPTest until the VE3 is incorporated into the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5151 348d0f76-0448-11de-a6fe-93d51630548a
Updated the FCP, the test, and the ADPR to handle an issue with the ADPR locating the yaml generated by the FCPTest.
Does not solve the ADPR error: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5126 348d0f76-0448-11de-a6fe-93d51630548a
Metrics of the new bams have changed slightly but should still fall within test toleraneces.
Will reset metrics in a later checkin after confirming changes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5125 348d0f76-0448-11de-a6fe-93d51630548a
Defaulting to the hour queue for running pipeline tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5122 348d0f76-0448-11de-a6fe-93d51630548a
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
Moved VariantEval validation from FCPTest to PipelineTest.
Cleaned up some duplicate code for writing temp files during tests.
Moved FCPTest to playground namespace to match move for FCP.q.
Added a basic HelloWorldPipelineTest for the HelloWorld QScript.
Moved duplicated error handling from JobRunners into the FunctionEdge.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5068 348d0f76-0448-11de-a6fe-93d51630548a
kshakir