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
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
Samuel Lee
Ron Levine
Valentin Ruano Rubio
Geraldine Van der Auwera
Yossi Farjoun
Steve Huang
samuelklee
Laura Gauthier
David Benjamin
meganshand
Chris Norman
Takuto Sato