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
Geraldine Van der Auwera
Valentin Ruano Rubio
Yossi Farjoun
Mark Fleharty
Ron Levine
David Benjamin
meganshand
Laura Gauthier
seru71
Yossi Farjoun
Takuto Sato