Also added the old model of indel calling to the FCP.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5749 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
See https://www.broadinstitute.org/gsa/wiki/index.php/GATK_resource_bundle
Which live locally in /humgen/gsa-hpprojects/GATK/bundle/current
You use this following command to create the bundle:
java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar dist/Queue.jar -S scala/qscript/core/GATKResourcesBundle.scala --gatkjarfile dist/GenomeAnalysisTK.jar -bsub -jobQueue gsa -svn 5660 $*
Annoyingly, it must be run in the trunk directory, and requires an explicit svn version number to create the directory. It also must be run in two stages manually. First, the local bundle is created, and then with the -phase2 argument all of the files in the local bundle are compressed and pushed to the FTP server. I'm likely going to shift most of my processes over to using this location for data file access, especially for b37 data sets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5665 348d0f76-0448-11de-a6fe-93d51630548a
- fixing a bug on single ended BWA option of the data processing pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5662 348d0f76-0448-11de-a6fe-93d51630548a
After viewing results on real case/control data from RAW -- it's really working quite well. ReadIndels, however, needs to use a T-test rather than a U-test, especially in deep coverage (at indel sites, the reads with indels will have mostly the same number of CIGAR indel elements -- one -- which doesn't really play nicely with the UTest when sample sets are large). Modified ReadsLargeInsertSize to be a two-way test (e.g. ReadsLarge and ReadsSmall). BaseQualityScore also suffers from the same issue as read indels, so switching over to a T-test in that case as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5653 348d0f76-0448-11de-a6fe-93d51630548a
+ UG now doesn't care whether it's given SNPs or indels to genotype, it will do the right thing -- so remove the option to specify which GM user wants
+ Max misamatches argument removed
integration test will follow
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5638 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
SGA updated to include new proportion-based insert size test.
Major fix for dichotomization test: MathUtils now optionally ignores NaN values for sums, averages, variances. In the future this feature can be pushed back into the AssociationContext object iself (e.g. no data? no entry), but it's kept like this for transparency for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5618 348d0f76-0448-11de-a6fe-93d51630548a
Implicit conversions for String to/from File.
Small updates to the example QScripts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5614 348d0f76-0448-11de-a6fe-93d51630548a
QuickCCTest is my test script for the gatherer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5547 348d0f76-0448-11de-a6fe-93d51630548a
MDP: Removed ApplyVariantCut as it's no longer necessary with VQSR2.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5534 348d0f76-0448-11de-a6fe-93d51630548a
rpoplin
kshakir
carneiro
depristo
chartl
corin
hanna