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
Now, instead of stripping out the GQs for mono sites, we transfer them to the RGQ.
This is extremely useful for people who want to know how confident the hom ref genotype calls are.
Perhaps this is just what CRSP needs for pertinent negatives.
Note that I also changed the tool to no longer use the GenotypeSummaries annotation by default since
it was adding some seemingly unnecessary annotations (like mean GQ now that we keep the GQ around and
number of no-calls). Let me know if this was a mistake (although Laura gave me a thumbs up).
Using --breakBandsAtMultiplesOf N will ensure that no reference blocks span across
genomic positions that are multiples of N. This is especially important in the
case of scatter-gather where you don't want your scatter intervals to start in the
middle of blocks (because of a limitation in the way -L works in the GATK for VCF
records with the END tag).
For example, running with --breakBandsAtMultiplesOf 5 on this record:
1 69491 . G <NON_REF> . . END=69523 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
Will produce the following records:
1 69491 . G <NON_REF> . . END=69494 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
1 69495 . C <NON_REF> . . END=69499 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
1 69500 . T <NON_REF> . . END=69504 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
etc.
Added docs and a new test.
GenotypeGVCFs now has the ability to unique-ify samples so I can genotype together two different datasets containing the same sample
Modify InbreedingCoeff so that it works when genotyping uniquified samples
* TextCigarCodec.decode() is now static, and the getSingleton() method is gone
* MergingSamRecordIterator now wants a Collection<SamReader> rather than Collection<SAMFileReader> in the constructor
* SeekableBufferedStream now correctly reads the requested number of bytes, removed workaround in GATKBAMIndex
* Removed unused annotations (CCC and HWP)
* Renamed one of the two GC annotations to "IGC" (for Interval GC)
* Revved picard & htsjdk (GATK constants are now removed from htsjdk)
* PT 82046038
-- Active Region Traversal was using per sample limits on the number of reads that were too low, especially now that we are running one sample at a time. This caused issues with high confidence variants being dropped in high coverage data.
-- HaplotypeCallerGVCFIntegrationTest PL/annotation changes due to using more reads in those tests
-- Removed a CountReadsInActiveRegionsIntegrationTest test for excessive coverage because the read coverage no longer goes over the limits in ART
Story:
=====
- https://www.pivotaltracker.com/story/show/83803796
Changes:
=======
- From a fix maximum ploidy indel RCM likelihood cache to a
dynamically resizable one.
- Used the occassion to removed an unused and deprecated method from ReferenceConfidenceModel
Testing:
=======
- Added integration test to check on ploidies larger than the previous limit of 20.
Add multi-allele test for info field annotations
Fix to process all types of INFO annotations
roll back to previous version, removes INFO and FORMAT
Correct @return for VariantAnnotatorEngine.getNonReferenceAlleles()
Enhance comments and clean up multi-allelic logic, handle header info number = R
only parse counts of A & R
Add INFO for AC
update MD5
Performance enhancement, only parse multiallelic with a count A or R
Make argument final in getNonReferenceAlleles()
Code cleanup, add exceptions for bad expression/allele size mismatch and missing header info for an expression
Change exception to warning for expression value/number of alleles check
remove adevertised exceptions
Story:
=====
- https://www.pivotaltracker.com/story/show/83259038
Changes:
=======
- Done minimal changes to make the fix after an arduous attempt to understand
CombineGVCFs code.
Test:
====
- Added a integration test to explicitly test for the bug.
- Updated a md5 changes as the bug was actually affecting one of the existing
integration tests.
* PT 84242218
* Note that FORMAT fields behave the same as INFO fields - if the annotation has a count of A (one entry per Alt Allele), it is split across the multiple output lines. Otherwise, the entire list is output with each field
Story:
-----
- https://www.pivotaltracker.com/story/show/83800586
Changes:
-------
- In GVCFWriter GQ is now recalculated out of the fianl PL array for the block.
Testing:
-------
- Updated affected integration test md5s
Ron Levine
Geraldine Van der Auwera
Yossi Farjoun
Laura Gauthier
Phillip Dexheimer
Eric Banks
rpoplin
Khalid Shakir
Valentin Ruano-Rubio
Ron Levine