fef63ce6a8
Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization.
...
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
...
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
...
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.
...
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
...
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
...
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).
...
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
...
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
...
- 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.
...
Closes issue #1340
2016-05-26 15:04:52 -04:00
25fa25b618
Added option to validate gvcf (for ValidateVariants) ( #1379 )
...
* 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
...
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
...
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
...
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
...
Addresses issue #1356
2016-05-19 08:15:30 -04:00
f5456a3761
Fixed M2 max alt alleles threshold evaluation error
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
e5c5804141
Modify MD5s to correct RankSum annotations
2016-03-01 14:05:51 -05:00
625941dc50
Merge pull request #1290 from broadinstitute/rhl_sac_nonref
...
StrandAlleleCountsBySample selects most likely only from VCF alleles
2016-02-29 17:05:57 -05:00
5e2ffc188b
Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194
...
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
80a22aad77
StrandAlleleCountsBySample selects most likely only from VCF alleles
2016-02-29 12:41:55 -05:00
c7e0f5b225
Removes Dithering from Rank Sum Test
...
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
243a0fcb74
Allele-specific insert size ranksum annotation
2016-01-28 16:03:57 -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
ed933013fe
Remove variant contig order check
2016-01-16 19:32:28 -05:00
c57c32b915
Merge pull request #1270 from broadinstitute/eb_small_genotyping_optimizations
...
Small optimizations to the joint calling code.
2016-01-13 08:46:57 -05:00
ab2f541d1f
Small optimizations to the joint calling code.
...
Thanks to profiling I noticed that the determineCoefficient() method was being called too often.
Because it returns a constant result in half of the invocations, its value should be cached when possible.
Also, the various calls to getLog10Likelihoods() showed up in the profiler, so I pulled those out too.
All told, it speeds up the genotyping by about 10 percent according to the profiler.
2016-01-12 21:48:20 -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
204cad3646
Remove "mem_free" from resident memory request params for Queue because it doesn't work and wouldn't actually reserve memory anyway
2016-01-08 10:27:56 -05:00
d16ed98c9e
Backport maxNoCall functionality from GATK4
2016-01-06 11:09:38 -05:00
1d72ab099c
Merge pull request #1247 from broadinstitute/ldg_VQSRmodelOutput
...
Add optional argument for VQSR to output the model to a file as a GAT…
2016-01-05 08:35:18 -05:00
fa1d90d236
Merge consecutive SNPs on the same read
2016-01-04 13:48:59 -05:00
2ddc48914e
Add optional argument for VQSR to output the model to a file as a GATKReport
...
GATKReport output also has mean and variance for annotation normalization info
2016-01-04 08:37:08 -05:00
71c6709765
Merge pull request #1145 from broadinstitute/ldg_M2_HapMapSensitivity
...
Fix no-normal bug; add HapMap sensitivity benchmarking
2016-01-04 08:27:37 -05:00
aa5e88a393
Fix exception when writing gVCF to stdout
2015-12-29 15:30:53 -05:00
eb6bdb2a62
MQ of Mate RankSum annotation
...
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
f9e9d2e273
Fix no-normal bug; add HapMap sensitivity benchmarking
2015-12-22 08:29:01 -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
bf875974d1
Prep MuTect2 and ContEst for release
...
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
5a3756410c
Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest
...
Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-23 17:08:30 -05:00
b0730c2b81
Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237
...
Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 13:58:20 -05:00
a7748368f8
Yet more doc improvements prior to 3.5 release
...
Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 10:59:24 -05:00
46ba0e519e
Restore FindCoveredIntervals + add docs
2015-11-22 10:19:04 -05:00
22fa1511be
Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192
...
Deprecate tools that were outdated or redundant
2015-11-21 14:58:00 -05:00
1cf66addaa
Deprecate tools that were outdated or redundant
...
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.
...
See issues referenced by the pull request for details.
2015-11-20 22:44:46 -05:00
1443ee8c7f
Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-20 11:23:02 -05:00
ccaddefa19
Validate VCF with sequence dictionary
2015-11-20 09:23:24 -05:00
Valentin Ruano Rubio
Samuel Lee
Ron Levine
Laura Gauthier
Takuto Sato
Steve Huang
meganshand
Geraldine Van der Auwera
Yossi Farjoun
samuelklee
David Benjamin
Chris Norman
Eric Banks
Mark Fleharty
Mark Fleharty