68b6f8f638
Replace VariantContextWriterFactory with VariantContextWriterBuilder
2016-11-30 16:04:25 -05:00
055d653bc2
Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406
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Fix adapter bounday for positive strand
2016-11-18 10:25:46 -05:00
22d94a7096
Fix adapter bounday for positive strand
2016-11-16 16:41:17 -05:00
6156b85ad9
Fixed logic error and tidied AlleleBalance and AlleleBalanceBySample
2016-11-16 14:10:48 -05:00
d61b4c7e91
Change the truth VCF
2016-11-15 14:56:15 -05:00
2b83dd7c5b
Added TreeReduce interface to VariantFiltration
2016-11-14 17:19:44 -05:00
bcbd7fe952
Change default value of STANDARD_CONFIDENCE_FOR_CALLING to 10
2016-11-11 02:06:41 -05:00
df0ba2ce8d
BaseCountsBySample counting bases at a particular position
2016-11-08 13:31:05 -05:00
029632eb1c
backport numerics changes in new qual
2016-11-01 03:16:21 -04:00
cc91052e69
fixed a max priority Q error while removing alt alleles when faced with high ploidy and allele count; added hackish integration test ( #1457 )
2016-10-27 11:19:49 -04:00
01a858542f
Remove RankSumTest and RMSAnnotation from hom-ref sites
2016-10-14 11:34:54 -04:00
16417bbf34
Fixes NaN issue in new Qual calculator
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Fixes issue #1491
2016-10-11 16:03:06 -04:00
81a9ece45b
deprecate -stand_emit_conf
2016-10-09 10:24:09 -04:00
4ef396f72e
Assign correct ambiguity code for * allele
2016-09-22 11:02:44 -04:00
318bee2269
Backport new AFCalculator
2016-09-21 15:21:56 -04:00
c13e3752d6
Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
2016-09-16 16:36:52 -04:00
6564066de3
Remove NON_REF from allSites VCF output
2016-09-16 13:55:52 -04:00
091d05370b
Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices ( #1475 )
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* alt alle removal by likelihoods now robust to ref allele indices (no longer assumes 0-indexed ref)
2016-09-13 21:20:44 -04:00
a7b1130224
Do not emit GVCF block definitions in the header
2016-09-09 07:41:03 -04:00
956b18fbb7
Make ReadPosRankSumTest.isUsableRead() account for deletions
2016-09-07 13:52:09 -04:00
3c88e6859f
fix 1430 for genotype filters; refactored filter() method; added unit and integration test; more comprehensive fix must be done first on htsjdk side in JEXLMap ( #1456 )
2016-09-06 17:30:18 -04:00
601c26a592
More small refactorings of Mutect2 code
2016-08-29 12:45:13 -04:00
a883905101
Remove -stand_emit_conf argument
2016-08-26 22:09:11 -04:00
bc3b3ac0ec
Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs.
2016-08-26 14:12:05 -04:00
4aede99697
Merge pull request #1453 from broadinstitute/db_mutect2
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Lots of small improvements to Mutect2 code
2016-08-23 18:35:38 -04:00
cd5c04f806
Make getElementForRead() in RankSumTest robust
2016-08-23 14:56:32 -04:00
01142dfb1c
Lots of small improvements to Mutect2 code
2016-08-23 09:50:48 -04:00
abc4d5b7b3
Bypass spanning deletions in Rank Sum tests
2016-08-17 14:02:22 -04:00
3510906c7f
addresses issue #1280 now interval padding works for exclude intervals
2016-08-10 13:45:45 -04:00
49507faaa3
Changed maximum allowed GQB value to 100.
2016-08-05 13:06:31 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
832a383acd
Fixed MD5 broken by PR #1440 .
2016-07-27 13:51:20 -04:00
9a6ce7a347
Merge pull request #1440 from broadinstitute/sl_issue_1345
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Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
2016-07-26 14:55:59 -04:00
fef63ce6a8
Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization.
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Addresses issue #1439 (thus #1437 ).
Fixes a bug where non informative PLs were not handled appropriatelly when calculating multi-allelic site QUAL values.
This was resulting in long execution times for very large datasets (~200,000 samples in the case of ExAC2).
2016-07-25 17:19:03 -04:00
3daed9e5a1
Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
2016-07-20 16:48:59 -04:00
7392c4d1b0
Removed spanning deletions if the deletion was removed
2016-07-19 12:23:49 -04:00
641382eb8b
Fix BetaTestingAnnotation group
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Add test
2016-07-13 16:05:21 -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
45607d1b30
RCM Variant sites merger won't output PL when there are too many alleles in order to avoid memory issues with large cohort runs.
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Small additional "cosmetic" changes to the code
Addresses issue #1419 .
2016-07-01 11:33:07 -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
4066bcd75c
Add new annotator for M1 clustered read position filter and M1 strand bias filter.
2016-06-29 22:46:37 -04:00
1b921666a7
Change to max value of ExcessHet
2016-06-29 16:33:50 -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
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
857459e420
Silly mistake '<' for a '<='. It was causing the exception when the exact number of alleles to drop was matching MAX_DROPPED_ALTERNATIVE_ALLELES_TO_LOG exactly (fixed to 20).
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I change the code to impose a maximum allele list message length instead and in the process I fixed the bug.
2016-06-17 15:22:59 -04:00
e119feee61
Added regression test for genotyping of spanning deletions in GenotypeGCVFs.
2016-06-15 09:48:26 -04:00
ba2e7be05b
Add integration test using -maxNumPLValues for GenotypeGVCFs
2016-06-07 14:38:12 -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
b95b76b0e2
Merge pull request #1394 from broadinstitute/gvda_add_colt_dependency
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Add colt > cern.jet.normal dependency
2016-06-01 14:16:57 -04:00
bd2626bea2
Add colt > cern.jet.normal dependency
2016-06-01 13:24:50 -04:00
30665c7dbc
Move Move htsjdk and picard to version 2.4.1
2016-05-31 22:36:38 -04:00
a76cb052e2
Ability to retry building VQSR model (contributed by mdp)
2016-05-31 18:57:55 -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
efbbbb1bd9
Add M2 to the HC annotations check
2016-05-27 13:49:31 -04:00
c4a06ad20a
Move indel realignment 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
e1fadae139
Fix error in InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator
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Same issue noticed in GATK4 [here](https://github.com/broadinstitute/gatk/issues/1856 )
2016-05-25 17:23:26 -04:00
2c8356519c
Merge pull request #1375 from broadinstitute/gvda_fix_offbyone_maxAltAlls_M2_#1297
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Fixed M2 max alt alleles threshold evaluation error
2016-05-19 13:59:02 -04:00
7fdd3c2a0c
Merge pull request #1358 from broadinstitute/sl_issue_1327
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Changed calls with GQ=0 to no-call for HaplotypeCaller in normal mode.
2016-05-19 12:26:35 -04:00
644076b1e1
Add fix and test for finalizing MQ annotation at BP resolution for variant and ref samples
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Addresses issue #1356
2016-05-19 08:15:30 -04:00
f5456a3761
Fixed M2 max alt alleles threshold evaluation error
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Also clarified some argument docs
2016-05-18 21:54:30 -04:00
bf4b1a5421
Changed calls for GQ=0 from 0/0 to ./. for HaplotypeCaller in normal mode.
2016-05-18 13:17:27 -04:00
35a06879f1
Move htsjdk and picard to version 2.3.0
2016-05-16 14:50:00 -04:00
8623830267
Fixed bug in which consecutive SPAN_DELS were merged into a ** MNP.#
2016-05-06 01:36:14 -04:00
aa0c76a166
Merge pull request #1326 from broadinstitute/sl_issue_1293
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Added maxNumPLValues argument to allow users to set maximum number of PL values in output.
2016-04-28 10:52:27 -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
e08940a5a8
Added maxNumPLValues argument to allow users to set maximum number of PL values in output.
2016-04-26 23:30:25 -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
509400495b
Changes edge case calculation for RankSumTest #1341
2016-04-22 14:41:05 -04:00
c040da427d
Replace string literals for annotation groups. Closes #1216 .
2016-04-19 15:54:44 -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
d573fc4adf
Add some comments to AFCalculationResult
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Add note that VC may be null (in this case because there are too many alts)
Add todo for possible inefficient code
2016-04-04 09:35:54 -04:00
68b068d2b3
Merge pull request #1329 from broadinstitute/cn_murmur_hash
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Use older version of murmur hash implementation included in gatk…
2016-03-31 13:00:43 -04:00
edc1b20132
Output a summary of WARN messages
2016-03-29 11:39:18 -04:00
017828e4b7
Use the older murmur hash implementation that is included in the gatk jar.
2016-03-29 10:20:44 -04:00
c81795cf50
Fix license in DroppedReadsTracker.
2016-03-22 13:39:13 -04:00
a8ebf21ac3
Implementation of dropped read tracking.
2016-03-21 18:36:29 -04:00
b873467756
Merge pull request #1321 from broadinstitute/rhl_fix_hr_logger_name
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Change logger class to HomopolymerRun
2016-03-16 11:44:40 -04:00
5c0e97def4
Change logger class to HomopolymerRun
2016-03-16 10:01:21 -04:00
9ffdfeccd5
Add test case for fix
2016-03-15 11:06:48 -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
6d7ec7377c
Set --reference_window_stop if homopolymer is greater than window size
2016-03-14 18:09:41 -04:00
c81d5b898e
Clarify VQSR inputs documentation
2016-03-11 16:38:33 -05:00
4990ed706a
Fixup for licensing update
2016-03-11 16:23:02 -05:00
6308b0f036
Add MuTect2 Tumor-only test.
2016-03-11 09:10:43 -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
28cfb06513
Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation
2016-03-09 08:22:58 -05:00
d9f9bd1d56
Add classes from "annotation party" to BetaTesting group
2016-03-09 08:17:44 -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
Ron Levine
David Benjamin
Geraldine Van der Auwera
Steve Huang
Valentin Ruano Rubio
Takuto Sato
Peter Fan
Samuel Lee
Andrii Nikitiuk
samuelklee
Laura Gauthier
meganshand
Yossi Farjoun
Chris Norman