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
* The value of this element (default true) determines whether Queue will explicitly run this walker over unmapped reads
* This patch fixes a runtime error when FindCoveredIntervals was used with Queue
* PT 81777160
* 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
-- Ignore SNP matches that lie outside the clipped read window
-- This fixes an issue where GATK would skip the entire read if a SNP is entirely
contained within a sequencing adapter.
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
Phillip Dexheimer
Eric Banks
Valentin Ruano Rubio
Laura Gauthier
Ron Levine
rpoplin
Khalid Shakir
Geraldine Van der Auwera
Ron Levine