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  • b6908f52f0 Merge pull request #1432 from broadinstitute/rhl_invalid_intervals Ron Levine 2016-07-15 13:02:39 -0400
  • 4f2e312805 Throw an exception for invalid Picard intervals Ron Levine 2016-07-07 10:24:20 -0400
  • c406102e03 Merge pull request #1436 from broadinstitute/ldg_fixBetaTestingAnnotationGroup ldgauthier 2016-07-13 16:23:19 -0400
  • 641382eb8b Fix BetaTestingAnnotation group Add test Laura Gauthier 2016-06-01 12:29:14 -0400
  • 5255435f0e Merge pull request #1433 from broadinstitute/rhl_progress_meter_periodicity Ron Levine 2016-07-13 10:14:01 -0400
  • aace73e884 Enable control of reporting periodicity Ron Levine 2016-07-08 12:46:50 -0400
  • 5e39b59ef3 Merge pull request #1429 from broadinstitute/ts_readpos_filter Takuto Sato 2016-07-12 08:30:51 -0400
  • d6d0678b50 Build on Laura's code and finish porting MuTect1 clustered read position filter. Takuto Sato 2016-06-15 15:32:17 -0400
  • 77d8da6bb2 Merge pull request #1431 from broadinstitute/sl_issue_1345 samuelklee 2016-07-06 11:46:39 -0700
  • 9b32cf5291 Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel. Samuel Lee 2016-06-21 21:44:27 -0400
  • 2c94f74a95 Merge pull request #1404 from broadinstitute/ldg_M2_addM1filters Takuto Sato 2016-07-05 13:27:35 -0400
  • 9c3b928945 Merge pull request #1428 from broadinstitute/vrr_issue_1419_out_of_mem_genotype_gvcfs Valentin Ruano Rubio 2016-07-01 13:58:38 -0400
  • 45607d1b30 RCM Variant sites merger won't output PL when there are too many alleles in order to avoid memory issues with large cohort runs. Small additional "cosmetic" changes to the code Addresses issue #1419. Valentin Ruano Rubio 2016-06-30 11:41:03 -0400
  • 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 Steve Huang 2016-06-30 22:36:49 -0400
  • 6471bda0cd Merge pull request #1426 from broadinstitute/ms_excessHetSmallP meganshand 2016-06-30 08:26:01 -0400
  • 63e0865491 Built on Laura's code to port the strand bias filter from M1 and refactored code aroud SomaticGenotypingEngine. Added a new integration test. Takuto Sato 2016-01-13 16:06:57 +0900
  • 4066bcd75c Add new annotator for M1 clustered read position filter and M1 strand bias filter. Laura Gauthier 2015-07-30 08:30:15 -0400
  • 1b921666a7 Change to max value of ExcessHet meganshand 2016-06-28 14:23:39 -0400
  • db196e709a Merge pull request #1424 from broadinstitute/ms_rankSumBug meganshand 2016-06-29 13:26:28 -0400
  • 556cc69185 Fix for int overflow in RankSum calculation meganshand 2016-06-24 15:31:42 -0400
  • b14312a14d Merge pull request #1389 from broadinstitute/vrr_non_ref_likelihoods_to_median Valentin Ruano Rubio 2016-06-28 16:07:09 -0400
  • 07052ba8ea Changes to use the median rather than the second best likelihood for the NON_REF allele Valentin Ruano Rubio 2016-05-26 14:59:26 -0400
  • b80a293848 Merge pull request #1422 from broadinstitute/rhl_htsjdk_picard_2.5.0 Ron Levine 2016-06-28 12:16:04 -0400
  • 3c5eac8c17 Move htsjdk and picard to version 2.5.0 Ron Levine 2016-06-27 19:43:06 -0400
  • 23c48bcdb1 Merge pull request #1415 from broadinstitute/shlee-addsupplementarytodocument Geraldine Van der Auwera 2016-06-23 22:11:25 -0400
  • 6fe80d53d0 Improve documentation sooheelee 2016-06-23 16:20:00 -0400
  • 4eff18a470 Merge pull request #1414 from broadinstitute/rhl_sv_hashmap Ron Levine 2016-06-23 12:22:43 -0400
  • c6ef81b611 Change HashMap to LinkedHashMap for predictable ordering Ron Levine 2016-06-23 10:48:22 -0400
  • 679941c1b1 Merge pull request #1412 from broadinstitute/sl_issue_1285 samuelklee 2016-06-22 15:25:19 -0400
  • 76bb8fd9e5 Allows GatherBqsrReports to accept a .list file as input. Samuel Lee 2016-06-20 13:30:39 -0400
  • ae8ab33cdd Merge pull request #1408 from broadinstitute/rhl_sv_non_diploids Ron Levine 2016-06-21 13:52:07 -0400
  • 427645162b SelectVariants works with non-diploids Ron Levine 2016-06-13 11:39:46 -0400
  • d3862459e9 Merge pull request #1410 from broadinstitute/vrr_bug_1407_no_such_element_exception Valentin Ruano Rubio 2016-06-20 15:52:25 -0400
  • 857459e420 Silly mistake '<' for a '<='. It was causing the exception when the exact number of alleles to drop was matching MAX_DROPPED_ALTERNATIVE_ALLELES_TO_LOG exactly (fixed to 20). I change the code to impose a maximum allele list message length instead and in the process I fixed the bug. Valentin Ruano Rubio 2016-06-17 11:46:25 -0400
  • 6b04f6ae14 Merge pull request #1405 from broadinstitute/sl_issue_1281 samuelklee 2016-06-15 13:59:14 -0400
  • e119feee61 Added regression test for genotyping of spanning deletions in GenotypeGCVFs. Samuel Lee 2016-06-07 10:36:03 -0400
  • 050bcbb06b Merge pull request #1403 from broadinstitute/rhl_ggvcf_max_num_pls Ron Levine 2016-06-08 12:54:19 -0400
  • ba2e7be05b Add integration test using -maxNumPLValues for GenotypeGVCFs Ron Levine 2016-06-07 14:38:12 -0400
  • f0f482c1fe - added an option to merge GenomeLocs that are abutting (contiguous) rather than actually overlapping. (#1399) Yossi Farjoun 2016-06-06 11:46:15 -0400
  • 85dce75f3f Update pom versions to mark the start of GATK 3.7 development Geraldine Van der Auwera 2016-06-01 17:21:48 -0400
  • f185a75e1c Update pom versions for the 3.6 release Geraldine Van der Auwera 2016-06-01 17:08:17 -0400
  • 6ba2e38a5c Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2016-06-01 17:04:21 -0400
  • b95b76b0e2 Merge pull request #1394 from broadinstitute/gvda_add_colt_dependency Geraldine Van der Auwera 2016-06-01 14:16:57 -0400
  • bd2626bea2 Add colt > cern.jet.normal dependency Geraldine Van der Auwera 2016-06-01 13:24:50 -0400
  • 8b24e3bd65 Merge pull request #1391 from broadinstitute/rhl_htsjdk_picard_2.4.1 Geraldine Van der Auwera 2016-06-01 06:49:16 -0400
  • 30665c7dbc Move Move htsjdk and picard to version 2.4.1 Ron Levine 2016-05-29 09:32:39 -0400
  • 801aa49d25 Merge pull request #1392 from broadinstitute/gvda_vqsr_retries_mdp Geraldine Van der Auwera 2016-05-31 21:35:27 -0400
  • a76cb052e2 Ability to retry building VQSR model (contributed by mdp) Geraldine Van der Auwera 2016-05-31 18:57:55 -0400
  • e2634e56a9 Merge pull request #1387 from broadinstitute/gvda_gatkdocs_enhancements Geraldine Van der Auwera 2016-05-31 17:15:18 -0400
  • d87345cd1d GATKDocs overhaul Geraldine Van der Auwera 2016-05-27 19:47:32 -0400
  • f77735cdde Merge pull request #1388 from broadinstitute/gvda_disable_phone_home Geraldine Van der Auwera 2016-05-27 19:55:57 -0400
  • 0769c8ae3e Remove Phone Home Geraldine Van der Auwera 2016-05-27 15:02:43 -0400
  • 15f3f902f7 Merge pull request #1374 from broadinstitute/gvda_move_ReassignOriginalMQAfterIndelRealignment_toPublic_#1364 Geraldine Van der Auwera 2016-05-27 16:07:14 -0400
  • efbbbb1bd9 Add M2 to the HC annotations check Geraldine Van der Auwera 2016-05-27 13:48:27 -0400
  • 5b80c92cb7 Improved article linking in error messages Geraldine Van der Auwera 2016-05-27 12:19:59 -0400
  • 3cc7d7e56d Hide deletion arguments in ASEReadCounter Geraldine Van der Auwera 2016-05-27 11:59:54 -0400
  • 81d4eaea29 Fixed warnings in LAATV and ValidateVariants Geraldine Van der Auwera 2016-05-27 11:49:48 -0400
  • c4a06ad20a Move indel realignment to public Geraldine Van der Auwera 2016-05-27 11:45:28 -0400
  • 3b7e0c56bf Moved post-IR MQ reverter filter to public Geraldine Van der Auwera 2016-05-18 00:03:36 -0400
  • e74a41e158 Merge pull request #1377 from broadinstitute/vrr_non_ref_likelihood_recal Valentin Ruano Rubio 2016-05-26 22:35:53 -0400
  • 9d32dec9cd Fix for the sum(AD) > DP bug. Valentin Ruano Rubio 2016-04-25 01:15:46 -0400
  • 25fa25b618 Added option to validate gvcf (for ValidateVariants) (#1379) Yossi Farjoun 2016-05-26 06:42:45 -0400
  • e1fadae139 Fix error in InfiniteRandomMatingPopulationModel.getLikelihoodsCalculator Steve Huang 2016-05-25 17:23:26 -0400
  • 2c8356519c Merge pull request #1375 from broadinstitute/gvda_fix_offbyone_maxAltAlls_M2_#1297 Geraldine Van der Auwera 2016-05-19 13:59:02 -0400
  • 7fdd3c2a0c Merge pull request #1358 from broadinstitute/sl_issue_1327 samuelklee 2016-05-19 12:26:35 -0400
  • edd9fcb7e5 Merge pull request #1370 from broadinstitute/ldg_fixBQresMQ ldgauthier 2016-05-19 09:39:07 -0400
  • 644076b1e1 Add fix and test for finalizing MQ annotation at BP resolution for variant and ref samples Addresses issue #1356 Laura Gauthier 2016-05-04 16:43:33 -0400
  • f5456a3761 Fixed M2 max alt alleles threshold evaluation error Geraldine Van der Auwera 2016-05-18 00:25:13 -0400
  • ff532ed0cd Merge pull request #1352 from broadinstitute/mf_othersrequired Mark Fleharty 2016-05-18 15:14:59 -0400
  • bf4b1a5421 Changed calls for GQ=0 from 0/0 to ./. for HaplotypeCaller in normal mode. Samuel Lee 2016-04-12 17:35:26 -0400
  • d611c45806 Adding OtherArgumentRequired option to allow an argument to require an additional argument. Mark Fleharty 2016-04-22 14:28:02 -0400
  • 6feb67d519 Merge pull request #1372 from broadinstitute/gvda_docfix_CV_syntax Geraldine Van der Auwera 2016-05-17 12:49:37 -0400
  • 6d5b643a9d Fix tagging syntax Geraldine Van der Auwera 2016-05-17 08:42:49 -0400
  • 81a67d67f7 Merge pull request #1371 from broadinstitute/rhl_htsjdk_picard_2.2.2 Ron Levine 2016-05-16 20:57:35 -0400
  • 35a06879f1 Move htsjdk and picard to version 2.3.0 Ron Levine 2016-04-26 13:56:05 -0400
  • 8b338dd111 Merge pull request #1367 from broadinstitute/dr_fix_na12878kb_startup_script_part2 ldgauthier 2016-05-13 14:26:33 -0400
  • 878878f9a5 Replace broken tcsh NA12878 KB server startup script with working bash version David Roazen 2016-05-13 14:03:37 -0400
  • e34ec0fbbb Merge pull request #1334 from broadinstitute/db_issue_1294 David Benjamin 2016-05-12 16:37:33 -0400
  • 71a3447772 Yf tumor only (#1298) Yossi Farjoun 2016-05-12 15:26:04 -0400
  • 3ecaacd8ec Merge pull request #1366 from broadinstitute/dr_fix_na12878kb_startup_script ldgauthier 2016-05-12 15:12:17 -0400
  • 47e1cfc04a Fix NA12878KB startup script for Java 8 David Roazen 2016-05-12 15:10:09 -0400
  • 85e6f22c82 Merge pull request #1362 from broadinstitute/rhl_fix_q_md5s Ron Levine 2016-05-11 09:16:18 -0400
  • 831360fd0b Don't output program tag Ron Levine 2016-05-10 10:47:43 -0400
  • acabbba57b Merge pull request #1359 from broadinstitute/droazen-gatk4-implications droazen 2016-05-06 13:40:33 -0400
  • 58a471b0ed Add "GATK4 Implications" section to GATK3 pull request template droazen 2016-05-06 12:46:27 -0400
  • 8623830267 Fixed bug in which consecutive SPAN_DELS were merged into a ** MNP.# David Benjamin 2016-03-31 22:46:42 -0400
  • aa0c76a166 Merge pull request #1326 from broadinstitute/sl_issue_1293 samuelklee 2016-04-28 10:52:27 -0400
  • a826cc7365 Merge pull request #1346 from broadinstitute/db_issue_945 David Benjamin 2016-04-27 21:54:50 -0400
  • aecaa6d38e Allow GenotypeGVCFs to emit ref sites. David Benjamin 2015-11-09 12:48:40 -0500
  • 2904572fc5 Merge pull request #1355 from broadinstitute/gvda_move_bqsrgatherer_to_public Geraldine Van der Auwera 2016-04-27 09:33:29 -0400
  • 14fe8b1e0e Moved BQSRGatherer and dependencies to the public module Geraldine Van der Auwera 2016-04-26 17:35:55 -0400
  • e08940a5a8 Added maxNumPLValues argument to allow users to set maximum number of PL values in output. Samuel Lee 2016-03-18 10:12:08 -0400
  • 46d41255ba Merge pull request #1284 from broadinstitute/rhl_htsjdk_picard_2.0.0 Ron Levine 2016-04-25 20:29:44 -0400
  • f337b45724 Move htsjdk and picard to version 2.0.0 Ron Levine 2016-04-25 13:15:40 -0400
  • 4e47db0320 Merge pull request #1350 from broadinstitute/gvda-fix_allelebalance_doc David Benjamin 2016-04-25 13:13:27 -0400
  • 662919e5fe Correction to AlleleBalance doc Geraldine Van der Auwera 2016-04-22 21:11:38 -0400
  • b54904dd42 Merge pull request #1349 from broadinstitute/ms_RankSum meganshand 2016-04-22 16:55:39 -0400
  • 509400495b Changes edge case calculation for RankSumTest #1341 meganshand 2016-04-08 16:33:03 -0400
  • 34a1b7d0b0 Merge pull request #1337 from broadinstitute/db_issue_1121 David Benjamin 2016-04-22 10:47:31 -0400
  • f639564599 Fixed bug in which PrintReads left out @PG header record David Benjamin 2016-04-02 22:36:54 -0400