4f2e312805
Throw an exception for invalid Picard intervals
2016-07-15 11:20:53 -04:00
641382eb8b
Fix BetaTestingAnnotation group
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Add test
2016-07-13 16:05:21 -04:00
aace73e884
Enable control of reporting periodicity
2016-07-13 07:24:03 -04:00
d6d0678b50
Build on Laura's code and finish porting MuTect1 clustered read position filter.
2016-07-11 17:33:08 -04:00
9b32cf5291
Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel.
2016-07-06 10:08:08 -04:00
2c94f74a95
Merge pull request #1404 from broadinstitute/ldg_M2_addM1filters
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MuTect 2: port strand artifact filter from MuTect 1
2016-07-05 13:27:35 -04:00
1ff234e7dd
remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
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remove alt alleles, when genotype count is explosively large, based on alleles' highest supporting haplotype score; max tolerable genotype count is controlled by a default value overridable by user
2016-06-30 22:36:49 -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
556cc69185
Fix for int overflow in RankSum calculation
2016-06-29 12:02:13 -04:00
07052ba8ea
Changes to use the median rather than the second best likelihood for the NON_REF allele
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Addresses issue #1378 following the first proposal using the 'median' rather than the 'mean'.
2016-06-28 13:10:22 -04:00
3c5eac8c17
Move htsjdk and picard to version 2.5.0
2016-06-28 09:42:32 -04:00
6fe80d53d0
Improve documentation
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Clarified that this also filters supplementary alignments.
2016-06-23 16:20:00 -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
30665c7dbc
Move Move htsjdk and picard to version 2.4.1
2016-05-31 22:36:38 -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
0769c8ae3e
Remove Phone Home
2016-05-27 16:16:29 -04:00
5b80c92cb7
Improved article linking in error messages
2016-05-27 13:49:31 -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
3b7e0c56bf
Moved post-IR MQ reverter filter to public
2016-05-27 12:39:58 -04:00
9d32dec9cd
Fix for the sum(AD) > DP bug.
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Closes issue #1340
2016-05-26 15:04:52 -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
d611c45806
Adding OtherArgumentRequired option to allow an argument to require an additional argument.
2016-05-17 16:31:41 -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
71a3447772
Yf tumor only ( #1298 )
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* tumor only pipeline
* a few new wrappers for picard tools
2016-05-12 15:26:04 -04:00
831360fd0b
Don't output program tag
2016-05-10 20:45:44 -04:00
aecaa6d38e
Allow GenotypeGVCFs to emit ref sites.
2016-04-27 15:53:44 -04:00
14fe8b1e0e
Moved BQSRGatherer and dependencies to the public module
2016-04-27 07:15:28 -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
509400495b
Changes edge case calculation for RankSumTest #1341
2016-04-22 14:41:05 -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
0eba8822e2
Change HashMap to LinkedHashMap for predictable iteration
2016-04-10 20:10:38 -04:00
e4003bc792
Add informative exceptions to getSAMFileSamples()
2016-03-31 13:41:11 -04:00
edc1b20132
Output a summary of WARN messages
2016-03-29 11:39:18 -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
b471884d97
Added run-time information to log output
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Also updated copyright date
2016-03-11 16:43:03 -05:00
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
5e2ffc188b
Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194
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Correct error messages and error handling in multiple tools
2016-02-29 17:05:24 -05:00
40a5adf767
Change error output to use the correct argument
2016-02-29 13:21:03 -05:00
c7e0f5b225
Removes Dithering from Rank Sum Test
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Fixing empty group case
Fixing MD5s
First comments addressed
Added permutation test
Adding new RankSum to AS_RankSum
Speeding up permutation algorithm and updating MD5s
Missed a few tests
Addressing comments
Changing md5s
2016-02-29 11:45:27 -05:00
7896055be3
- Fixed bug in GenomeLoc parser
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- Added a warning when two contigs are too similar that it might cause problems with parsing
- Added tests of modified parser and of warning.
2016-02-02 06:53:22 -05:00
8ab2eef6f0
Merge pull request #1282 from broadinstitute/ts_annotation
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Allele specific insert size ranks sum annotation
2016-01-29 18:13:46 -05:00
243a0fcb74
Allele-specific insert size ranksum annotation
2016-01-28 16:03:57 -05:00
1e4a98827c
Merge pull request #1278 from broadinstitute/gvda-expose_queue_setting
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Expose time between checks as CLI argument (Queue)
2016-01-28 11:00:36 -05:00
5592e4ead0
Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecalibration) in an allele-specific manner
2016-01-22 13:18:21 -05:00
a46a4a6175
Expose time between checks for whether new jobs can be submitted as a user-settable parameter on CLi. Useful when testing pipelines to make idle time shorter. Contributed by @dakl (Daniel Klevebring on GATK forum).
2016-01-22 12:13:07 -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
ed933013fe
Remove variant contig order check
2016-01-16 19:32:28 -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
eb6bdb2a62
MQ of Mate RankSum annotation
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Intermediate commit for tests
Adding tests
Fixing tests after rebase
Fixing one MD5
Fixing documentation
Removing annotation from standard group
Adding documentation
2015-12-23 10:24:40 -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
46ba0e519e
Restore FindCoveredIntervals + add docs
2015-11-22 10:19:04 -05:00
08a9c80559
Make the header sequence dictionary match reference
2015-11-21 19:12:37 -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
0b3b09e3ff
Move htsjdk & picard to version 1.141
2015-11-20 16:26:26 -05:00
ccaddefa19
Validate VCF with sequence dictionary
2015-11-20 09:23:24 -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
3d1dc303b3
Merge pull request #1197 from broadinstitute/ts_ve_nullPointer
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Prevent null pointer exception in PrintMissingComp module
2015-11-02 14:42:50 -05:00
33462c7b50
Removed the line that caused a null pointer, as the information it logged was not useful. Updated docs and added an integration test to ensure the code no longer throws the exception.
2015-11-02 12:45:09 -05:00
f7eb5d3082
Enable family-level stratification (if a ped file is provided)
2015-10-28 09:55:04 -04:00
4fbcfc2e36
Merge pull request #1173 from broadinstitute/ldg_AS_annotations
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New map-combine-finalize annotation framework
2015-10-27 12:04:56 -04:00
19af5724c5
Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden
2015-10-27 09:44:26 -04:00
fcaf37279c
Finished draft of code for new map-combine-reduce annotation framework
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All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
2015-10-27 09:23:29 -04:00
36ca9fe898
Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
2015-10-25 20:33:56 -04:00
0d936b28c4
Merge pull request #1178 from broadinstitute/ms_ROCCurve
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ROCCurve High Confidence Mode
2015-10-22 09:19:13 -04:00
795fe75886
Update doc for multiallelics, trimming is the default behavior
2015-10-22 04:04:09 -04:00
a57500b2fc
ROCCurve High Confidence Mode
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Integration Tests
Updated test
Changed method
Minor changes
Changed whitespace
Fixed uncalled counts and 0 in R
Fixed ReadBackedPileUp
Removed imports and changed MD5
Fixed failing test
Adding vqslod color
Updating script to create KB
Fixing integration test now that the KB is bigger
Adressing comments
2015-10-21 21:30:54 -04:00
df7a482335
VariantAnnotator now supports annotating FILTER field from an external resource.
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Updated the docs.
2015-10-14 14:26:21 -04:00
e776502c49
Fix Sample mergeValues failure when merging identical string values ( #1156 ).
2015-10-12 09:56:05 -04:00
2bcded11cb
VariantAnnotator checks alleles when annotationg with external resource
2015-10-08 17:01:30 -04:00
033115eae0
Move htsjdk & picard to version 1.140
2015-10-08 10:42:05 -04:00
622ec352bb
Fix for combining records in which one has a spanning deletion and needs a padded reference allele.
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This was erroring out and not working.
2015-10-02 16:28:16 -04:00
Ron Levine
Laura Gauthier
Takuto Sato
Samuel Lee
Steve Huang
meganshand
Valentin Ruano Rubio
sooheelee
Yossi Farjoun
Geraldine Van der Auwera
Mark Fleharty
David Benjamin
seru71
Yossi Farjoun
Chris Norman
Eric Banks