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)
- ASEReadCounter (public tool) replce Tuuli's script to produce the input to Manny's tool.
It count the number of reads that support the ref allele and the alt allele, filtereing low qual reads and bases and keep only properPaired reads
- ASECaller (private tool) take both RNA and DNA, and produce ontingencyTables ** still under development **
minor changes in other tools:
- update RNA HC variant calling scala script
- expose FS method pValueForContingencyTable to be able to call it from ASEcaller
In ASEReadCounter:
- allow different option to deal with overlaping read from the same fragment
- add option to ignore or include indels in the pileups
- add option to disabled DuplicateRead
add ASEReadCounterIntegrationTest.java and files for the test
fixed NPE when normal contains no reads
first integration test (micro) and unit tests, also rename of MuTectHC -> M2
adding in standard GATK license terms
incorporated HOSTILE mode to PCR Error Correction
removed tumor and normal name parameters and cleaned up internal name handling
changes to allow for calling without a matched normal (technically, not true 'tumor-only' calling). Used for panel-of-normals creation
additional regression tests, based on DREAM data. Removed accidental addition of TandemRepeatAnnotator to default annotations
updated MD5 based on run from GSA4 to fix bamboo issue
reverted unneeded visibility changes
Geraldine Van der Auwera
droazen
Laura Gauthier
Eric Banks
Ron Levine
kshakir
Khalid Shakir
Yossi Farjoun
kcibul
Alex Baumann
Ami Levy-Moonshine
Phillip Dexheimer