f6c18a5182
Throw an exception if the BQSR input covariants file is not found
2016-08-11 12:46:14 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
641382eb8b
Fix BetaTestingAnnotation group
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Add test
2016-07-13 16:05:21 -04:00
63e0865491
Built on Laura's code to port the strand bias filter from M1 and refactored code aroud SomaticGenotypingEngine. Added a new integration test.
2016-06-29 22:46:40 -04:00
3c5eac8c17
Move htsjdk and picard to version 2.5.0
2016-06-28 09:42:32 -04:00
c6ef81b611
Change HashMap to LinkedHashMap for predictable ordering
2016-06-23 10:48:22 -04:00
76bb8fd9e5
Allows GatherBqsrReports to accept a .list file as input.
2016-06-22 12:39:18 -04:00
427645162b
SelectVariants works with non-diploids
2016-06-21 12:26:13 -04:00
f0f482c1fe
- added an option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping. ( #1399 )
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- this should make ValidateVariants much faster.
- fixed NPE that occurs when there is no -L argument
2016-06-06 11:46:15 -04:00
85dce75f3f
Update pom versions to mark the start of GATK 3.7 development
2016-06-01 17:21:48 -04:00
f185a75e1c
Update pom versions for the 3.6 release
2016-06-01 17:08:17 -04:00
d87345cd1d
GATKDocs overhaul
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- Fixed displaying of default values
- Removed code cruft
- Reorganized tooldoc categories and improved names
- Reorganized tools within categories where applicable
- Touched up various tool docs
- Switched default gatkdocs output to html
- Added parameter in agrregator pom to control output type
- Set gatkdocs publishing script to output php
- Deprecated GenotypeAndValidate walker
- Added back PhoneHome arguments with @Deprecated annotations
2016-05-29 16:35:08 -04:00
3cc7d7e56d
Hide deletion arguments in ASEReadCounter
2016-05-27 12:46:13 -04:00
81d4eaea29
Fixed warnings in LAATV and ValidateVariants
2016-05-27 12:46:02 -04:00
c4a06ad20a
Move indel realignment to public
2016-05-27 12:39:58 -04:00
25fa25b618
Added option to validate gvcf (for ValidateVariants) ( #1379 )
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* with option --gvcf CLP will now put extra checks that a gvcf must adhere to (existance of <NON_REF> allele at every variant, and that the variants in total cover the entire requested intervals, or the whole genome if no intervals have been specified)
* works on gvcf produced by HC when using either GVCF or BP_RESOLUTION mode
* added positive and negative tests
2016-05-26 06:42:45 -04:00
6d5b643a9d
Fix tagging syntax
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Syntax was given as -V:format,name but should be -V:name,format
2016-05-17 08:42:49 -04:00
35a06879f1
Move htsjdk and picard to version 2.3.0
2016-05-16 14:50:00 -04:00
f337b45724
Move htsjdk and picard to version 2.0.0
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Conflicts:
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
2016-04-25 14:51:25 -04:00
662919e5fe
Correction to AlleleBalance doc
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Addresses https://github.com/broadinstitute/dsde-docs/issues/818
The equations representing the allele balance calculation were confusing and inconsistent with both the description text and the code. This doc change brings consistency and correctness.
Also improves the AB by sample doc accordingly.
2016-04-25 12:10:01 -04:00
f639564599
Fixed bug in which PrintReads left out @PG header record
2016-04-22 08:46:18 -04:00
cfbf062f29
fixed bug in dbSNP binding in VariantAnnotationEngine
2016-04-21 14:38:31 -04:00
e2828104b1
SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall
2016-04-17 10:24:05 -04:00
e4003bc792
Add informative exceptions to getSAMFileSamples()
2016-03-31 13:41:11 -04:00
31fc64f82c
To address weird case with all hom-refs, but alt allele is present, skip AS_QD for all-ref sites and remove raw annotations whether or not they can be successfully finalized
2016-03-15 09:34:47 -04:00
4990ed706a
Fixup for licensing update
2016-03-11 16:23:02 -05:00
d0432713e0
Merge pull request #1311 from broadinstitute/ldg_BetaTestAnnotationsGroup
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Add classes from "annotation party" to BetaTesting group
2016-03-11 08:13:32 -05:00
16ef36088e
Merge pull request #1308 from broadinstitute/gvda_fix_license_quotes_#1307
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Update licenses
2016-03-10 12:37:53 -05:00
d9f9bd1d56
Add classes from "annotation party" to BetaTesting group
2016-03-09 08:17:44 -05:00
244a217ee7
Fix sample_gene_summary reports header order
2016-03-08 22:21:51 -05:00
dcc6c0f2aa
Merge pull request #1306 from broadinstitute/rhl_doc_overlapping_genes
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Output coverage for all overlapping genes in DepthOfCoverage
2016-03-08 13:28:30 -05:00
9a306ca221
Update licenses
2016-03-05 01:09:43 -08:00
2b70f14740
Misc documentation improvements
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Added caveat to VariantFiltration documentation
Fixed PON creation example in M2 doc
Improved MalformedReadFilter doc
Updated N CIGAR error message
2016-03-03 15:48:54 -08:00
4d203b895a
added support for overlapping exons/genes in DepthOfCoverage
2016-03-03 15:09:54 -05:00
40a5adf767
Change error output to use the correct argument
2016-02-29 13:21:03 -05:00
c93a611ea3
Remove unneeded dependency
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Addresses https://github.com/broadgsa/gatk/pull/15 for Guillermo
2016-01-21 16:51:01 -05:00
593c9ddf01
Allow VariantsToTable to evaluate the type of each split variant when -F TYPE and -SMA are specified
2016-01-12 08:12:29 -05:00
d16ed98c9e
Backport maxNoCall functionality from GATK4
2016-01-06 11:09:38 -05:00
9c8f035780
LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid
2015-12-14 10:42:32 -05:00
4767a83d8a
Update pom versions to mark the start of GATK 3.6 development
2015-11-25 01:52:51 -05:00
9749adf22a
Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201
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Prep MuTect2 for release
2015-11-24 20:12:57 -05:00
bf875974d1
Prep MuTect2 and ContEst for release
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Renamed M2 to MuTect2
Renamed ContaminationWalker to ContEst
Refactored related tests and usages (including in Queue scripts)
Moved M2 and ContEst + accompanying classes from private to protected
Made QSS a StandardSomaticAnnotation (new annotation group/interface) to prevent it from being sucked in with the rest of the StandardAnnotation group
2015-11-24 16:43:20 -05:00
88a0514ec7
Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
2015-11-23 17:53:19 -05:00
22fa1511be
Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192
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Deprecate tools that were outdated or redundant
2015-11-21 14:58:00 -05:00
1cf66addaa
Deprecate tools that were outdated or redundant
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ReadAdaptorTrimmer (unsound and untested)
BaseCoverageDistribution (redundant with DiagnoseTargets)
CoveredByNSamplesSites (redundant with DiagnoseTargets)
FindCoveredIntervals (redundant with DiagnoseTargets)
VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests)
LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106 ) (use Picard liftover tool)
sortByRef.pl (use Picard SortVCF)
ListAnnotations (useless)
Also deleted the java archive from the private repository (old junk we never use)
2015-11-20 22:49:40 -05:00
2570cab24c
Assorted documentation fixes, enhancements and reorganization.
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See issues referenced by the pull request for details.
2015-11-20 22:44:46 -05:00
4da0d1300c
adding fraction informative reads annotation.
2015-11-18 08:39:47 -05:00
25b8ba45f4
More allele-specific annotations: AS_QD and AS_InbreedingCoeff
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Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
Also refactored code shared by ExcessHet and InbreedingCoeff
2015-11-09 16:38:31 -05:00
e4627ed5c3
Addressing comments
2015-11-04 11:00:01 -05:00
b5165b8d30
Fix for out of date VCF version output
2015-11-03 17:35:47 -05:00
Ron Levine
Andrii Nikitiuk
Laura Gauthier
Takuto Sato
Samuel Lee
Yossi Farjoun
Geraldine Van der Auwera
David Benjamin
seru71
meganshand
Yossi Farjoun