61875e4dfa
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
2017-02-22 17:57:59 -05:00
1d36d9fd69
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
2017-02-17 07:03:03 -05:00
e86da63d04
Update pom versions to mark the start of GATK 3.8 development
2016-12-12 08:53:23 -05:00
56f2c1ac75
Update pom versions for the 3.7 release
2016-12-12 08:49:43 -05:00
b42dc1624b
Documentation fixes
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- Fix missing closing code block tag
- SOR fix + minor fix to template
- Minor typo fixes
- Make no_cmdline_in_header arg visible in docs
- Caveats for UG-only args that are difficult to move out of common collection
- Reference -L and -XL in -gvcf documentation
- Annotation doc fixes (dsde-docs#1289)
- Unhide some ContEst args and make Advanced
- Fix inputPrior error message
- Update web urls
- Add JEXL doc link
2016-12-05 14:09:44 -05:00
262c08aee3
Make exit system file type message generic
2016-11-23 10:12:21 -05:00
22d94a7096
Fix adapter bounday for positive strand
2016-11-16 16:41:17 -05:00
2d06f33227
Set HTSJDK log level
2016-11-15 07:08:19 -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
d7090ef158
Write saved WARN messages to stderr instead of stdout
2016-10-21 13:01:07 -04:00
cfd3ffa2c0
Replace SAMFileReader with calls to SamReaderFactory
2016-10-14 11:22:54 -04:00
318bee2269
Backport new AFCalculator
2016-09-21 15:21:56 -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
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
4f2e312805
Throw an exception for invalid Picard intervals
2016-07-15 11:20:53 -04:00
aace73e884
Enable control of reporting periodicity
2016-07-13 07:24:03 -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
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
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
3c5eac8c17
Move htsjdk and picard to version 2.5.0
2016-06-28 09:42:32 -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
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
5b80c92cb7
Improved article linking in error messages
2016-05-27 13:49:31 -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
aecaa6d38e
Allow GenotypeGVCFs to emit ref sites.
2016-04-27 15:53:44 -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
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
9a306ca221
Update licenses
2016-03-05 01:09:43 -08:00
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
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
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
Ron Levine
Geraldine Van der Auwera
David Benjamin
Peter Fan
Andrii Nikitiuk
Takuto Sato
Samuel Lee
Steve Huang
meganshand
Valentin Ruano Rubio
Yossi Farjoun
Mark Fleharty
Yossi Farjoun
Laura Gauthier