Previously, if a SNP occurred in sample A at a position that was in the middle of a deletion for sample B,
sample B would be genotyped as homozygous reference there (but it's NOT reference - there's a deletion).
Now, sample B is genotyped as having a symbolic DEL allele.
Minor cleanup added. Note that I also removed Laura's previous fix for this problem.
Existing integration tests change because I've added a new header line to the VCF being output.
I also added several tests for the new functionality showing:
1. genotyping from separate and already combined gvcfs give the same output
2. genotyping over multiple spanning deletions works
3. combining works too
Existing unit tests also cover this case.
New unit test for deprecated mergeVariantsViaLD
Update HaplotypeCallerIntegrationTest.java
Delete duplicate testHaplotypeCallerMergeVariantsViaLDException test.
Exclude MQ0BySample
Move SD and TRA to new StandardUGAnnotation interface
There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.
Fairly minor if plentiful fixes to various gatkdocs. Merging this without formal review since all tests pass, the gatkdocs build, and no one really wants to review corrections to grammar, typos and layout for 120+ documents. Review will be done by users in production ;-)
When -qsub-broad is specified instead of -qsub, use the "h_vmem" parameter
instead of "h_rss" to specify memory limit requests.
Also cause the GridEngine native arguments to be output by default to the logger,
instead of only when in debug mode.
fix blasted license blurbs
updates based on PR comments (abstractify HaplotypeCallerArgumentCollection into AssemblyBasedCallerArgumentCollection)
comments on comments from PR review
The GATK command line header keys were being repeated in the VCF and
subsequently lost to a single key value by HTSJDK. This resolves
the issue by appending the name of the walker after the text
"GATKCommandLine" and a number after that if the same walker was
used more than once in the form: GATKCommandLine.(walker name) for
the first occurrence of the walker, and GATKCommandLine.(walker name).#
where # is the number of the occurrence of the walker (e.g.
GATKCommandLine.SomeWalker.2 for the second occurrence of SomeWalker).
Integration test added to EngineFeaturesIntegrationTest to verify
two runs of same walker follow expected form.
Resolves#909
See also: HTSJDK #43
Build a ReferenceContext in ActiveRegionWalkers to pass in to annotation engine so we can call the TandemRepeatAnnotator from M2
Make TandemRepeatAnnotator default annotation for M2.
Setup (but don't use yet) HC-style contamination downsampling.
New HC integration test with TandemRepeatAnnotator
In the process of realignment we add +10 to the MQ of each realigned read, breaking the MQ 60 cap. That may contribute to problems observed by Bertrand (a step in the ROC curve plot of the VQSR results)
Ron Levine
Geraldine Van der Auwera
Eric Banks
Joseph White
ldgauthier
droazen
kshakir
Khalid Shakir
Yossi Farjoun
kcibul
Alex Baumann
Ami Levy-Moonshine
Phillip Dexheimer