de3ca65232
Bumping HTSJDK version to pickup a bug fix for CRAM.
2015-01-26 14:47:39 -03:00
e26e55efe1
Merge pull request #802 from broadinstitute/pd_selectvariants_subset
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Added -trimAlternates argument to SelectVariants
2015-01-22 05:05:42 -05:00
72f76add71
Added -trimAlternates argument to SelectVariants
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* PT 84021222
* -trimAlternates removes all unused alternate alleles from variants. Note that this is pretty aggressive for monomorphic sites
2015-01-21 21:33:35 -05:00
d209699485
Merge pull request #804 from broadinstitute/jt_read_filters
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Allows users to disable the DuplicateReadFilter
2015-01-21 15:45:48 -05:00
5ce34d81b8
Allows users to disable specific read filters from the command line
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- enable this for DuplicateReadFilter only
- enable the @DisabledReadFilters annotation to do this at the Walker level
2015-01-21 13:17:29 -05:00
7102477168
Merge pull request #798 from broadinstitute/rhl_split_n_cigar_reads_exception
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Rhl split n cigar reads exception
2015-01-15 00:20:49 -05:00
804b2a36b7
Fix SplitNCigar reads exception by making the list of RNAReadTransformer non-abstract, add test for -fixNDN
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Includes documentation changes for -fixNDN argument and the read transformer documentation.
Documentation changes to CombineVariants
2015-01-14 22:22:05 -05:00
0292d49842
Merge pull request #801 from broadinstitute/pd_gatkvcfconstants
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Collected VCF IDs and header lines into one place
2015-01-14 09:43:48 -05:00
8599132713
Merge pull request #800 from broadinstitute/ldg_CGPpedError
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Address user-reported bug featuring "trio" family with two children, one...
2015-01-14 09:35:33 -05:00
6190d660e0
Edits to work with the latest htsjdk release:
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* 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
2015-01-13 21:32:10 -05:00
b73e9d506a
Added GATKVCFConstants and GATKVCFHeaderLines to consolidate the GATK-specific VCF annotations
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* 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
2015-01-13 21:32:09 -05:00
6b2bd5ed09
Address user-reported bug featuring "trio" family with two children, one parent
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Add test to cover case with family of one parent, two children
2015-01-13 18:35:44 -05:00
cf4ac4a388
Merge pull request #799 from broadinstitute/rp_fix_active_region_downsampling
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Raising per-sample limits on the number of reads in ART and HC.
2015-01-09 12:45:58 -05:00
2e5f9db758
Raising per-sample limits on the number of reads in ART and HC.
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-- 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
2015-01-09 11:21:42 -05:00
03203e249e
Merge pull request #792 from broadinstitute/rhl_pairhmm_log_stderr
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Rhl pairhmm log stderr
2015-01-07 12:41:10 -05:00
99ff5fb75b
Merge pull request #797 from broadinstitute/vrr_ploidy_limitation_removal
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MERGE AFTER TEST PASS: Fixes explicit limitation of the maximum ploidy of the reference-confide...
2015-01-07 12:38:19 -05:00
aae04b6122
Fixes explicit limitation of the maximum ploidy of the reference-confidence model
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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.
2015-01-07 10:43:22 -05:00
7d58544f17
Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml
2015-01-06 10:32:11 -05:00
ef32c44688
Merge pull request #795 from broadinstitute/ldg_VQSRcmdlineOutput
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VQSR VCF header command line now contains annotations and tranche levels
2015-01-05 14:59:04 -05:00
1d5996dd1d
Merge pull request #796 from broadinstitute/rp_update_bundle_Axiom_poly
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Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resou...
2015-01-05 14:53:45 -05:00
10b23bfb04
Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resource bundle because it is used in the v3.3 best practices
2015-01-05 14:52:31 -05:00
26c46ae05e
Change logger.info to logger.error
2015-01-05 14:14:02 -05:00
b4fda38922
Use logging system instead of stderr
2015-01-05 14:04:10 -05:00
e28ee24fc6
Update private single sample pipeline script
2015-01-05 12:11:21 -05:00
88b6f3aa50
Change []-type arrays to lists so argument parsing works in VCF header commandline output
2015-01-05 10:21:06 -05:00
3240b3538a
Merge pull request #794 from broadinstitute/rhl_read_backed_phasing
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Rhl read backed phasing
2015-01-05 09:47:25 -05:00
6f566a0e66
Merge pull request #793 from broadinstitute/mf_xhmm_add_genotyping
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Add option to genotype additional user-defined interval lists
2015-01-05 09:46:06 -05:00
ac10b9c3cd
Merge pull request #791 from broadinstitute/ldg_fixCGPbug
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Add error handling for genotypes that are called but have no PLs
2015-01-05 09:40:38 -05:00
c6840124fe
clean up, add final
2015-01-04 23:01:24 -05:00
85dc703461
Add TestMergeIntoMNP() and TestReallyMergeIntoMNP()
2015-01-01 09:51:20 -05:00
bb94833750
Add more tests
2014-12-30 22:45:44 -05:00
714d575e3b
correct reference file name
2014-12-25 14:00:39 -05:00
a7fba5c209
restructure and add more tests
2014-12-25 13:57:54 -05:00
64375f6341
Messages that were going to stdout now going to stderr
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Make PairHMM outputs go to stderr instead of stdout
Change output from stdout to stderr in close()
Updated lib with output going to stderr
2014-12-23 11:03:29 -05:00
11cd0080c3
Add option to genotype additional user-defined interval lists
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Add Qscript 'ONLY_GENOTYPE_xhmmCNVpipeline' to genotype additional user-defined interval lists
Add Qscript 'ONLY_GENOTYPE_xhmmCNVpipeline' to genotype additional user-defined interval lists (and similar option to Qscript 'xhmmCNVpipeline')
2014-12-21 13:02:17 -05:00
069398ad46
Added more tests and documentation
2014-12-19 12:57:43 -05:00
a9694951d2
Add error handling for genotypes that are called but have no PLs
2014-12-18 15:03:20 -05:00
a4a9e73ec8
Merge pull request #789 from broadinstitute/gg_update_vqsr_example
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Updated VQSR tool docs
2014-12-18 13:32:15 -05:00
b0e615251b
Updated VQSR tool docs
2014-12-18 12:59:37 -05:00
4a2ac38308
Merge pull request #790 from broadinstitute/rp_nsubtil_fix-snp-detection
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BQSR bug fix from @nsubtil
2014-12-18 09:19:53 -05:00
071389b507
Merge pull request #785 from broadinstitute/rhl_variant_multiallelic_annotations
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Rhl variant multiallelic annotations
2014-12-18 09:11:42 -05:00
08790e1dab
Fix mmultiallelic info field annotation for VariantAnnotator
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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
2014-12-17 22:21:00 -05:00
ba949389c5
matchHaplotypeAlleles() no longer calls alleleSegregationIsKnown(), added a TODO to investigate
2014-12-17 14:02:24 -05:00
d84970ff75
BQSR bug fix from @nsubtil
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-- 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.
2014-12-17 10:04:37 -05:00
56f8e4f9cf
Add comments, alleleSegregationIsKnown() check is added to matchHaplotypeAlleles()
2014-12-17 03:25:26 -05:00
3deaa4832c
Merge pull request #788 from broadinstitute/ldg_fixCombineGVCFsBug
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Fixed huge bug from 9895005a (CombineGVCFs used to stop after the first ...
2014-12-16 15:17:33 -05:00
011843c569
Fixed huge bug from 9895005a (CombineGVCFs used to stop after the first contig)
2014-12-16 12:43:32 -05:00
bcc6b73e9b
Merge pull request #786 from broadinstitute/pd_variantstotable_sma
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Fix VariantsToTable output of FORMAT record lists when -SMA is specified
2014-12-16 10:37:22 -05:00
3d32babc29
Merge pull request #787 from broadinstitute/vrr_wrong_reference_base_bugfix
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Fixing CombineGVCFs that writes out the wrong REF allele
2014-12-16 10:35:47 -05:00
736a857e82
Fixing CombineGVCFs that writes out the wrong REF allele
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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.
2014-12-13 22:38:24 -05:00
Khalid Shakir
Valentin Ruano Rubio
Phillip Dexheimer
jmthibault79
Geraldine Van der Auwera
Ron Levine
rpoplin
Laura Gauthier
Menachem Fromer