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  • a43d2a7ed1 Merge pull request #1338 from broadinstitute/db_issue_1291 David Benjamin 2016-04-21 20:21:08 -0400
  • cfbf062f29 fixed bug in dbSNP binding in VariantAnnotationEngine David Benjamin 2016-04-03 21:22:07 -0400
  • 44691f036b Merge pull request #1333 from broadinstitute/db_issue_1216 David Benjamin 2016-04-19 21:55:18 -0400
  • c040da427d Replace string literals for annotation groups. Closes #1216. David Benjamin 2016-04-01 00:12:41 -0400
  • 70b259a3fb Merge pull request #1347 from broadinstitute/rhl_sv_vf_info_nocall Ron Levine 2016-04-19 10:59:53 -0400
  • e2828104b1 SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall Ron Levine 2016-04-13 13:42:03 -0400
  • 7e0a9e44fe Merge pull request #1344 from broadinstitute/rhl_contam_downsamp_map Ron Levine 2016-04-11 08:29:14 -0400
  • 0eba8822e2 Change HashMap to LinkedHashMap for predictable iteration Ron Levine 2016-04-08 18:45:25 -0400
  • 2baa7a0b9e Merge pull request #1339 from broadinstitute/ldg_documentGenotypingCode ldgauthier 2016-04-08 16:02:21 -0400
  • b4197f62f2 Merge pull request #1335 from broadinstitute/gvda_templates Geraldine Van der Auwera 2016-04-04 18:23:04 -0400
  • e6c8c378e8 Added issue and pull request templates Geraldine Van der Auwera 2016-04-01 23:52:45 -0400
  • 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 Laura Gauthier 2016-03-23 08:47:48 -0400
  • edbb7e7984 Merge pull request #1331 from broadinstitute/rhl_doc_null_ptr Ron Levine 2016-03-31 15:38:39 -0400
  • e4003bc792 Add informative exceptions to getSAMFileSamples() Ron Levine 2016-03-30 16:44:46 -0400
  • 68b068d2b3 Merge pull request #1329 from broadinstitute/cn_murmur_hash Geraldine Van der Auwera 2016-03-31 13:00:43 -0400
  • dcefbe3a2a Merge pull request #1323 from broadinstitute/rhl_output_warnings Ron Levine 2016-03-29 14:54:27 -0400
  • edc1b20132 Output a summary of WARN messages Ron Levine 2016-03-17 17:38:52 -0400
  • 017828e4b7 Use the older murmur hash implementation that is included in the gatk jar. Chris Norman 2016-03-29 10:20:44 -0400
  • ea615f8918 Merge pull request #1324 from broadinstitute/cn_droppedreads_license Chris Norman 2016-03-23 08:52:22 -0400
  • c81795cf50 Fix license in DroppedReadsTracker. Chris Norman 2016-03-22 13:39:13 -0400
  • b7ecd68f30 Merge pull request #1257 from broadinstitute/cn_dropped_reads Chris Norman 2016-03-22 09:16:15 -0400
  • a8ebf21ac3 Implementation of dropped read tracking. Chris Norman 2015-12-15 09:38:08 -0500
  • b873467756 Merge pull request #1321 from broadinstitute/rhl_fix_hr_logger_name Ron Levine 2016-03-16 11:44:40 -0400
  • cfc32b7419 Merge pull request #1320 from broadinstitute/ldg_AS_QD_fix ldgauthier 2016-03-16 10:21:38 -0400
  • 5c0e97def4 Change logger class to HomopolymerRun Ron Levine 2016-03-16 10:01:21 -0400
  • 9ffdfeccd5 Add test case for fix Laura Gauthier 2016-03-15 11:06:48 -0400
  • 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 Laura Gauthier 2016-03-14 13:17:29 -0400
  • 4efde50225 Merge pull request #1318 from broadinstitute/rhl_va_hrun_exception Ron Levine 2016-03-14 18:22:40 -0400
  • 6d7ec7377c Set --reference_window_stop if homopolymer is greater than window size Ron Levine 2016-03-11 20:39:54 -0500
  • 2baf7d8c4e Merge pull request #1314 from broadinstitute/yf_output_more_information_and_fix_copywrite_date Geraldine Van der Auwera 2016-03-12 22:48:15 -0500
  • b471884d97 Added run-time information to log output Yossi Farjoun 2016-03-10 09:53:26 -0500
  • 71d816d8f5 Merge pull request #1316 from broadinstitute/gvda_clarify_vqsr_input_doc Geraldine Van der Auwera 2016-03-11 16:40:30 -0500
  • c81d5b898e Clarify VQSR inputs documentation Geraldine Van der Auwera 2016-03-11 12:47:13 -0500
  • eeccc95a7a Merge pull request #1317 from broadinstitute/gvda_fix_licenses Geraldine Van der Auwera 2016-03-11 16:32:47 -0500
  • 4990ed706a Fixup for licensing update Geraldine Van der Auwera 2016-03-11 16:23:02 -0500
  • 1072afeb57 Merge pull request #1296 from broadinstitute/ts_addM2TomorOnlyTest Takuto Sato 2016-03-11 13:20:36 -0500
  • 6308b0f036 Add MuTect2 Tumor-only test. Takuto Sato 2016-02-24 15:06:57 -0500
  • d0432713e0 Merge pull request #1311 from broadinstitute/ldg_BetaTestAnnotationsGroup ldgauthier 2016-03-11 08:13:32 -0500
  • 16ef36088e Merge pull request #1308 from broadinstitute/gvda_fix_license_quotes_#1307 Geraldine Van der Auwera 2016-03-10 12:37:53 -0500
  • 643516b3b2 Merge pull request #1310 from broadinstitute/rhl_doc_sample_gene_summary_header Geraldine Van der Auwera 2016-03-09 09:12:36 -0500
  • 99532f40c1 Merge pull request #1312 from broadinstitute/ldg_fixASheaders ldgauthier 2016-03-09 08:46:34 -0500
  • 28cfb06513 Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation Laura Gauthier 2016-02-12 20:32:06 -0500
  • d9f9bd1d56 Add classes from "annotation party" to BetaTesting group Laura Gauthier 2016-03-09 08:17:44 -0500
  • 244a217ee7 Fix sample_gene_summary reports header order Ron Levine 2016-03-08 12:45:09 -0500
  • dcc6c0f2aa Merge pull request #1306 from broadinstitute/rhl_doc_overlapping_genes ldgauthier 2016-03-08 13:28:30 -0500
  • aa7a8e17df Merge pull request #1304 from broadinstitute/ldg_fixROCCurveHomRef ldgauthier 2016-03-07 11:50:40 -0500
  • 9a306ca221 Update licenses Geraldine Van der Auwera 2016-03-05 01:09:43 -0800
  • 7d2c56f681 Merge pull request #1299 from broadinstitute/gvda_doc_updates Geraldine Van der Auwera 2016-03-04 16:06:12 -0800
  • 2b70f14740 Misc documentation improvements Geraldine Van der Auwera 2016-02-27 13:11:17 -0500
  • 4d203b895a added support for overlapping exons/genes in DepthOfCoverage seru71 2016-01-29 14:30:43 +0100
  • 36a2297f79 Clarify how UNKNOWN truth sites are treated Laura Gauthier 2016-03-02 17:32:39 -0500
  • c1076bcc23 Reconcile ROC curve numbers with AssessNA12878: Exclude homRefs and no-calls, trim alleles, split het-non-refs Add arg to include unknowns as TPs in order to match AssessNA12878 Add in check for KB sites that are monomorphic in NA12878 Laura Gauthier 2016-02-29 13:32:32 -0500
  • 8c15d3ccd8 Merge pull request #1303 from broadinstitute/rhl_fix_test_ranksums ldgauthier 2016-03-01 16:09:29 -0500
  • e5c5804141 Modify MD5s to correct RankSum annotations Ron Levine 2016-03-01 14:05:51 -0500
  • 625941dc50 Merge pull request #1290 from broadinstitute/rhl_sac_nonref Ron Levine 2016-02-29 17:05:57 -0500
  • 5e2ffc188b Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194 Ron Levine 2016-02-29 17:05:24 -0500
  • 32bd02aa9d Merge pull request #1186 from broadinstitute/ms_RankSum meganshand 2016-02-29 14:10:37 -0500
  • 40a5adf767 Change error output to use the correct argument Ron Levine 2016-02-22 20:27:34 -0500
  • 80a22aad77 StrandAlleleCountsBySample selects most likely only from VCF alleles Ron Levine 2016-02-12 15:46:29 -0500
  • c7e0f5b225 Removes Dithering from Rank Sum Test meganshand 2015-10-21 09:27:52 -0400
  • 3b327ac0e4 Merge pull request #1273 from broadinstitute/yf_Fix_GATK_bug_around_hg38_contignames Yossi Farjoun 2016-02-02 07:10:58 -0500
  • 7896055be3 - Fixed bug in GenomeLoc parser - Added a warning when two contigs are too similar that it might cause problems with parsing - Added tests of modified parser and of warning. Yossi Farjoun 2016-01-16 22:37:12 -0500
  • 8ab2eef6f0 Merge pull request #1282 from broadinstitute/ts_annotation ldgauthier 2016-01-29 18:13:46 -0500
  • 243a0fcb74 Allele-specific insert size ranksum annotation Takuto Sato 2015-11-02 09:40:10 -0500
  • 1e4a98827c Merge pull request #1278 from broadinstitute/gvda-expose_queue_setting Geraldine Van der Auwera 2016-01-28 11:00:36 -0500
  • 0e969d9c5d Merge pull request #1279 from broadinstitute/ldg_removeExtraKBsamples ldgauthier 2016-01-28 08:32:20 -0500
  • 633e729608 Reverted setupNA12878kb script to use old-style path names Import files are now derived from /humgen/gsa-hpprojects/NA12878Collection/knowledgeBase/runme.allLoci.csh, which subsets samples to NA12878 but maintains all loci Laura Gauthier 2016-01-22 15:22:09 -0500
  • ab5a8f0bb0 Merge pull request #1266 from broadinstitute/ldg_VQSRforAlleles ldgauthier 2016-01-22 13:19:11 -0500
  • 5592e4ead0 Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecalibration) in an allele-specific manner Laura Gauthier 2015-12-07 08:38:20 -0500
  • a46a4a6175 Expose time between checks for whether new jobs can be submitted as a user-settable parameter on CLi. Useful when testing pipelines to make idle time shorter. Contributed by @dakl (Daniel Klevebring on GATK forum). Geraldine Van der Auwera 2016-01-21 14:40:58 -0500
  • 76817fe5ec Merge pull request #1276 from broadinstitute/gvda-remove_unneeded_dependency Geraldine Van der Auwera 2016-01-21 16:51:34 -0500
  • c93a611ea3 Remove unneeded dependency Geraldine Van der Auwera 2016-01-20 15:28:41 -0500
  • 98eba7fb53 Merge pull request #1272 from broadinstitute/rhl_rm_variant_contig_order_check Ron Levine 2016-01-20 09:32:10 -0500
  • ed933013fe Remove variant contig order check Ron Levine 2016-01-15 21:10:10 -0500
  • c57c32b915 Merge pull request #1270 from broadinstitute/eb_small_genotyping_optimizations Eric Banks 2016-01-13 08:46:57 -0500
  • ab2f541d1f Small optimizations to the joint calling code. Eric Banks 2016-01-11 22:22:37 -0500
  • d1565e4e6f Merge pull request #1261 from broadinstitute/ldg_VariantsToTableMultiallelicTypes ldgauthier 2016-01-12 10:47:22 -0500
  • 593c9ddf01 Allow VariantsToTable to evaluate the type of each split variant when -F TYPE and -SMA are specified Laura Gauthier 2015-12-10 10:17:41 -0500
  • 7f7ba446c0 Merge pull request #1269 from broadinstitute/dr_repair_3.5_tag Geraldine Van der Auwera 2016-01-08 16:06:33 -0500
  • dc5c08f940 Repair 3.5 tag in unstable by merging the missing 3.5 commit from stable David Roazen 2016-01-08 15:33:15 -0500
  • d9e0b7ba58 Merge pull request #1268 from broadinstitute/ldg_fixQueueTests3 ldgauthier 2016-01-08 12:58:46 -0500
  • 204cad3646 Remove "mem_free" from resident memory request params for Queue because it doesn't work and wouldn't actually reserve memory anyway Laura Gauthier 2016-01-08 10:27:56 -0500
  • f002acebdf Merge pull request #1264 from broadinstitute/rhl_max_nocall_1262 Ron Levine 2016-01-06 14:54:24 -0500
  • d16ed98c9e Backport maxNoCall functionality from GATK4 Ron Levine 2015-12-28 12:23:14 -0500
  • 1d72ab099c Merge pull request #1247 from broadinstitute/ldg_VQSRmodelOutput ldgauthier 2016-01-05 08:35:18 -0500
  • 37746e40f4 Merge pull request #1263 from broadinstitute/rhl_rbp_not_merging_snps Ron Levine 2016-01-04 15:37:04 -0500
  • fa1d90d236 Merge consecutive SNPs on the same read Ron Levine 2015-12-14 12:11:07 -0500
  • 2ddc48914e Add optional argument for VQSR to output the model to a file as a GATKReport GATKReport output also has mean and variance for annotation normalization info Laura Gauthier 2015-11-20 15:28:46 -0500
  • 71c6709765 Merge pull request #1145 from broadinstitute/ldg_M2_HapMapSensitivity ldgauthier 2016-01-04 08:27:37 -0500
  • 4b3b5636c6 Merge pull request #1265 from broadinstitute/rhl_hc_stdout_1259 Ron Levine 2015-12-29 23:07:53 -0500
  • aa5e88a393 Fix exception when writing gVCF to stdout Ron Levine 2015-12-29 15:02:42 -0500
  • 7089824e1b Merge pull request #1251 from broadinstitute/ms_annotations meganshand 2015-12-23 12:36:43 -0500
  • eb6bdb2a62 MQ of Mate RankSum annotation meganshand 2015-10-29 15:32:00 -0400
  • f9e9d2e273 Fix no-normal bug; add HapMap sensitivity benchmarking Laura Gauthier 2015-09-01 08:09:38 -0400
  • 0c3c775566 Merge pull request #1248 from broadinstitute/rhl_keep_gt Ron Levine 2015-12-14 12:19:49 -0500
  • 9c8f035780 LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid Ron Levine 2015-10-20 13:46:03 -0400
  • 4767a83d8a Update pom versions to mark the start of GATK 3.6 development Geraldine Van der Auwera 2015-11-25 01:52:04 -0500
  • e91472ddc7 Update pom versions for the 3.5 release Geraldine Van der Auwera 2015-11-25 01:29:48 -0500
  • ee63b59b52 Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2015-11-25 01:27:41 -0500
  • 9749adf22a Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201 Geraldine Van der Auwera 2015-11-24 20:12:57 -0500