increased runtime java memory, changed default PON for NN to be new ICE PON
updated FP rates, when using new default PON. SNPs up by ~3%, INDELs down by 40%
updated git hash reference
updated git hash reference
added "str_contraction" artifact filter (improves specificity, especially in exomes)
refactored out VCF constants and added descriptions
added "artifact detection mode" for PON creation
added "str_contraction" artifact filter (improves specificity, especially in exomes)
added new dream evaulation markdown
added results for SMC 4
fixed up documentation, moved location to /dsde/working/mutect/dream_smc, and checked in scala script
added "artifact detection mode" for PON creation
added "str_contraction" artifact filter (improves specificity, especially in exomes)
fixed bug which would overwrite germline_risk filter errors
updated "how to" documents and records
fixed license text
thinned down FP regression test from 700 sites to 100. we have better ways (DREAM, NN) to check accuracy of the method and 100 is good enough to catch regressions
why oh why do the MD5-based unit tests produce different results on different machine architectures? I hate that :/
Thanks to GG, LDG and DR -- test should now produce the same results regardless of machine architecture
disabled downsampling... hopefully in the final attempt to make this work cross architecture!
enforced LOGLESS_CACHING... hopefully in the final final attempt to make this work cross architecture!
refactored out VCF constants and added descriptions
-We now pull htsjdk and picard from maven central.
-Updated the GATK codebase as necessary to adapt to changes in the Feature
interface.
-Since VCFHeader now requires that all header lines have unique keys, uniquified
the keys of GVCFBlock header lines by including the min/max GQ in the key.
Updated MD5s accordingly.
-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
In the case where there's a low quality SNP under a spanning deletion in the gvcfs:
if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still
emitting a record with just the symbolic DEL allele (because that allele is high quality).
We no longer do that.
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
Kristian Cibulskis
Geraldine Van der Auwera
Eric Banks
Sheila Chandran
Ron Levine
melonistic
David Roazen
Ami Levy-Moonshine
Joseph White
ldgauthier
kshakir
Khalid Shakir
Yossi Farjoun