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
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
a826cc7365
Merge pull request #1346 from broadinstitute/db_issue_945
...
Genotype GVCFs emits QUAL for ref sites.
2016-04-27 21:54:50 -04:00
aecaa6d38e
Allow GenotypeGVCFs to emit ref sites.
2016-04-27 15:53:44 -04:00
2904572fc5
Merge pull request #1355 from broadinstitute/gvda_move_bqsrgatherer_to_public
...
Moved BQSRGatherer and dependencies to the public module
2016-04-27 09:33:29 -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
46d41255ba
Merge pull request #1284 from broadinstitute/rhl_htsjdk_picard_2.0.0
...
Move htsjdk and picard to version 2.0.0
2016-04-25 20:29:44 -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
4e47db0320
Merge pull request #1350 from broadinstitute/gvda-fix_allelebalance_doc
...
Corrections to AlleleBalance (and AB by sample) docs
2016-04-25 13:13:27 -04:00
662919e5fe
Correction to AlleleBalance doc
...
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
b54904dd42
Merge pull request #1349 from broadinstitute/ms_RankSum
...
Fixes RankSum Small Sample Size Edge Case #1341
2016-04-22 16:55:39 -04:00
509400495b
Changes edge case calculation for RankSumTest #1341
2016-04-22 14:41:05 -04:00
34a1b7d0b0
Merge pull request #1337 from broadinstitute/db_issue_1121
...
Fixed bug in which PrintReads left out @PG header record
2016-04-22 10:47:31 -04:00
Geraldine Van der Auwera
Valentin Ruano Rubio
Yossi Farjoun
Steve Huang
samuelklee
ldgauthier
Mark Fleharty
Samuel Lee
Mark Fleharty
Ron Levine
David Roazen
David Benjamin
meganshand