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14258 Commits (e34ec0fbbba2dc1d424449ed30dc3b53e4ce6f6f)

Author SHA1 Message Date
David Benjamin 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
Yossi Farjoun 71a3447772 Yf tumor only (#1298) 
* tumor only pipeline
* a few new wrappers for picard tools
 2016-05-12 15:26:04 -04:00
ldgauthier 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
David Roazen 47e1cfc04a Fix NA12878KB startup script for Java 8 2016-05-12 15:10:09 -04:00
Ron Levine 85e6f22c82 Merge pull request #1362 from broadinstitute/rhl_fix_q_md5s 
Don't output program tag
 2016-05-11 09:16:18 -04:00
Ron Levine 831360fd0b Don't output program tag 2016-05-10 20:45:44 -04:00
droazen 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
droazen 58a471b0ed Add "GATK4 Implications" section to GATK3 pull request template 2016-05-06 13:39:47 -04:00
David Benjamin 8623830267 Fixed bug in which consecutive SPAN_DELS were merged into a ** MNP.# 2016-05-06 01:36:14 -04:00
samuelklee 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
David Benjamin 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
David Benjamin aecaa6d38e Allow GenotypeGVCFs to emit ref sites. 2016-04-27 15:53:44 -04:00
Geraldine Van der Auwera 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
Geraldine Van der Auwera 14fe8b1e0e Moved BQSRGatherer and dependencies to the public module 2016-04-27 07:15:28 -04:00
Samuel Lee e08940a5a8 Added maxNumPLValues argument to allow users to set maximum number of PL values in output. 2016-04-26 23:30:25 -04:00
Ron Levine 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
Ron Levine 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
David Benjamin 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
Geraldine Van der Auwera 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
meganshand 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
meganshand 509400495b Changes edge case calculation for RankSumTest #1341 2016-04-22 14:41:05 -04:00
David Benjamin 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
David Benjamin f639564599 Fixed bug in which PrintReads left out @PG header record 2016-04-22 08:46:18 -04:00
David Benjamin a43d2a7ed1 Merge pull request #1338 from broadinstitute/db_issue_1291 
Fixed bug in dbSNP binding in VariantAnnotationEngine.  Closes issue #1291.
 2016-04-21 20:21:08 -04:00
David Benjamin cfbf062f29 fixed bug in dbSNP binding in VariantAnnotationEngine 2016-04-21 14:38:31 -04:00
David Benjamin 44691f036b Merge pull request #1333 from broadinstitute/db_issue_1216 
Replace string literals for annotation groups.  Closes #1216
 2016-04-19 21:55:18 -04:00
David Benjamin c040da427d Replace string literals for annotation groups. Closes #1216. 2016-04-19 15:54:44 -04:00
Ron Levine 70b259a3fb Merge pull request #1347 from broadinstitute/rhl_sv_vf_info_nocall 
SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall
 2016-04-19 10:59:53 -04:00
Ron Levine e2828104b1 SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall 2016-04-17 10:24:05 -04:00
Ron Levine 7e0a9e44fe Merge pull request #1344 from broadinstitute/rhl_contam_downsamp_map 
Change HashMap to LinkedHashMap for predictable iteration order
 2016-04-11 08:29:14 -04:00
Ron Levine 0eba8822e2 Change HashMap to LinkedHashMap for predictable iteration 2016-04-10 20:10:38 -04:00
ldgauthier 2baa7a0b9e Merge pull request #1339 from broadinstitute/ldg_documentGenotypingCode 
Add some comments to AFCalculationResult
 2016-04-08 16:02:21 -04:00
Geraldine Van der Auwera b4197f62f2 Merge pull request #1335 from broadinstitute/gvda_templates 
Added issue and pull request templates
 2016-04-04 18:23:04 -04:00
Geraldine Van der Auwera e6c8c378e8 Added issue and pull request templates 2016-04-04 13:27:45 -04:00
Laura Gauthier d573fc4adf Add some comments to AFCalculationResult 
Add note that VC may be null (in this case because there are too many alts)
Add todo for possible inefficient code
 2016-04-04 09:35:54 -04:00
Ron Levine edbb7e7984 Merge pull request #1331 from broadinstitute/rhl_doc_null_ptr 
Add informative exceptions to getSAMFileSamples()
 2016-03-31 15:38:39 -04:00
Ron Levine e4003bc792 Add informative exceptions to getSAMFileSamples() 2016-03-31 13:41:11 -04:00
Geraldine Van der Auwera 68b068d2b3 Merge pull request #1329 from broadinstitute/cn_murmur_hash 
Use older version of murmur hash implementation included in gatk…
 2016-03-31 13:00:43 -04:00
Ron Levine dcefbe3a2a Merge pull request #1323 from broadinstitute/rhl_output_warnings 
Output a summary of WARN messages
 2016-03-29 14:54:27 -04:00
Ron Levine edc1b20132 Output a summary of WARN messages 2016-03-29 11:39:18 -04:00
Chris Norman 017828e4b7 Use the older murmur hash implementation that is included in the gatk jar. 2016-03-29 10:20:44 -04:00
Chris Norman ea615f8918 Merge pull request #1324 from broadinstitute/cn_droppedreads_license 
Fix license in DroppedReadsTracker.
 2016-03-23 08:52:22 -04:00
Chris Norman c81795cf50 Fix license in DroppedReadsTracker. 2016-03-22 13:39:13 -04:00
Chris Norman b7ecd68f30 Merge pull request #1257 from broadinstitute/cn_dropped_reads 
Implementation of dropped reads tracking for HC/Mutect.
 2016-03-22 09:16:15 -04:00
Chris Norman a8ebf21ac3 Implementation of dropped read tracking. 2016-03-21 18:36:29 -04:00
Ron Levine b873467756 Merge pull request #1321 from broadinstitute/rhl_fix_hr_logger_name 
Change logger class to HomopolymerRun
 2016-03-16 11:44:40 -04:00
ldgauthier cfc32b7419 Merge pull request #1320 from broadinstitute/ldg_AS_QD_fix 
To address weird case with all hom-refs, but alt allele is present, s…
 2016-03-16 10:21:38 -04:00
Ron Levine 5c0e97def4 Change logger class to HomopolymerRun 2016-03-16 10:01:21 -04:00
Laura Gauthier 9ffdfeccd5 Add test case for fix 2016-03-15 11:06:48 -04:00
Laura Gauthier 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