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