050bcbb06b
Merge pull request #1403 from broadinstitute/rhl_ggvcf_max_num_pls
...
Add integration test using -maxNumPLValues for GenotypeGVCFs
2016-06-08 12:54:19 -04:00
ba2e7be05b
Add integration test using -maxNumPLValues for GenotypeGVCFs
2016-06-07 14:38:12 -04:00
f0f482c1fe
- added an option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping. ( #1399 )
...
- 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
6ba2e38a5c
Merge remote-tracking branch 'unstable/master'
2016-06-01 17:04:21 -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
8b24e3bd65
Merge pull request #1391 from broadinstitute/rhl_htsjdk_picard_2.4.1
...
Move htsjdk and picard to version 2.4.1
2016-06-01 06:49:16 -04:00
30665c7dbc
Move Move htsjdk and picard to version 2.4.1
2016-05-31 22:36:38 -04:00
801aa49d25
Merge pull request #1392 from broadinstitute/gvda_vqsr_retries_mdp
...
Ability to retry building VQSR model (contributed by mdp)
2016-05-31 21:35:27 -04:00
a76cb052e2
Ability to retry building VQSR model (contributed by mdp)
2016-05-31 18:57:55 -04:00
e2634e56a9
Merge pull request #1387 from broadinstitute/gvda_gatkdocs_enhancements
...
GATKDocs overhaul
2016-05-31 17:15:18 -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
f77735cdde
Merge pull request #1388 from broadinstitute/gvda_disable_phone_home
...
Remove Phone Home
2016-05-27 19:55:57 -04:00
0769c8ae3e
Remove Phone Home
2016-05-27 16:16:29 -04:00
15f3f902f7
Merge pull request #1374 from broadinstitute/gvda_move_ReassignOriginalMQAfterIndelRealignment_toPublic_#1364
...
Code cleanup campaign pre-3.6; see itemized commit messages.
2016-05-27 16:07:14 -04:00
efbbbb1bd9
Add M2 to the HC annotations check
2016-05-27 13:49:31 -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
e74a41e158
Merge pull request #1377 from broadinstitute/vrr_non_ref_likelihood_recal
...
Fix for the sum(AD) > DP bug.
2016-05-26 22:35:53 -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
edd9fcb7e5
Merge pull request #1370 from broadinstitute/ldg_fixBQresMQ
...
Add fix and test for finalizing MQ annotation at BP resolution for va…
2016-05-19 09:39:07 -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
ff532ed0cd
Merge pull request #1352 from broadinstitute/mf_othersrequired
...
Adds othersRequired so that some arguments can require other arguments in order to work.
2016-05-18 15:14:59 -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
d611c45806
Adding OtherArgumentRequired option to allow an argument to require an additional argument.
2016-05-17 16:31:41 -04:00
6feb67d519
Merge pull request #1372 from broadinstitute/gvda_docfix_CV_syntax
...
Fix VCF tagging syntax in CombineVariants doc
2016-05-17 12:49:37 -04:00
6d5b643a9d
Fix tagging syntax
...
Syntax was given as -V:format,name but should be -V:name,format
2016-05-17 08:42:49 -04:00
81a67d67f7
Merge pull request #1371 from broadinstitute/rhl_htsjdk_picard_2.2.2
...
Move htsjdk and picard to version 2.3.0
2016-05-16 20:57:35 -04:00
35a06879f1
Move htsjdk and picard to version 2.3.0
2016-05-16 14:50:00 -04:00
8b338dd111
Merge pull request #1367 from broadinstitute/dr_fix_na12878kb_startup_script_part2
...
Replace broken tcsh NA12878 KB server startup script with working bash version
2016-05-13 14:26:33 -04:00
878878f9a5
Replace broken tcsh NA12878 KB server startup script with working bash version
2016-05-13 14:14:18 -04:00
e34ec0fbbb
Merge pull request #1334 from broadinstitute/db_issue_1294
...
Fixed treatment of SPAN_DEL in ReadBackedPhasing and MNF merging. Closes #1294 .
2016-05-12 16:37:33 -04:00
71a3447772
Yf tumor only ( #1298 )
...
* tumor only pipeline
* a few new wrappers for picard tools
2016-05-12 15:26:04 -04:00
3ecaacd8ec
Merge pull request #1366 from broadinstitute/dr_fix_na12878kb_startup_script
...
Fix NA12878KB startup script for Java 8
2016-05-12 15:12:17 -04:00
47e1cfc04a
Fix NA12878KB startup script for Java 8
2016-05-12 15:10:09 -04:00
85e6f22c82
Merge pull request #1362 from broadinstitute/rhl_fix_q_md5s
...
Don't output program tag
2016-05-11 09:16:18 -04:00
831360fd0b
Don't output program tag
2016-05-10 20:45:44 -04:00
acabbba57b
Merge pull request #1359 from broadinstitute/droazen-gatk4-implications
...
Add "GATK4 Implications" section to GATK3 pull request template
2016-05-06 13:40:33 -04:00
58a471b0ed
Add "GATK4 Implications" section to GATK3 pull request template
2016-05-06 13:39:47 -04:00
8623830267
Fixed bug in which consecutive SPAN_DELS were merged into a ** MNP.#
2016-05-06 01:36:14 -04:00
Ron Levine
Yossi Farjoun
Geraldine Van der Auwera
Valentin Ruano Rubio
Steve Huang
samuelklee
ldgauthier
Mark Fleharty
Samuel Lee
Mark Fleharty
David Roazen
David Benjamin