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  • bf875974d1 Prep MuTect2 and ContEst for release Geraldine Van der Auwera 2015-11-20 23:12:44 -0500
  • 1f8e45f0ba Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_downsample_1179 Geraldine Van der Auwera 2015-11-23 21:39:43 -0500
  • 88a0514ec7 Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings Geraldine Van der Auwera 2015-11-23 17:53:19 -0500
  • 5a3756410c Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest Mark Fleharty 2015-11-23 17:08:30 -0500
  • b0730c2b81 Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237 Geraldine Van der Auwera 2015-11-22 13:58:20 -0500
  • 0babe6abf7 Merge pull request #1241 from broadinstitute/gvda_undeprecate_FindCoveredIntervals_1240 Geraldine Van der Auwera 2015-11-22 13:56:25 -0500
  • a7748368f8 Yet more doc improvements prior to 3.5 release Geraldine Van der Auwera 2015-11-21 16:05:08 -0500
  • 46ba0e519e Restore FindCoveredIntervals + add docs Geraldine Van der Auwera 2015-11-22 10:03:06 -0500
  • 8f0ce02838 Merge pull request #1233 from broadinstitute/rhl_fix_example_bcf_dict Ron Levine 2015-11-21 21:45:16 -0500
  • 08a9c80559 Make the header sequence dictionary match reference Ron Levine 2015-11-20 21:25:25 -0500
  • 22fa1511be Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192 Geraldine Van der Auwera 2015-11-21 14:58:00 -0500
  • 592d43f3b3 Merge pull request #1209 from broadinstitute/gvda_yet_more_doc_fixes_1195 Geraldine Van der Auwera 2015-11-21 02:26:46 -0500
  • 1cf66addaa Deprecate tools that were outdated or redundant Geraldine Van der Auwera 2015-11-20 19:00:27 -0500
  • 2570cab24c Assorted documentation fixes, enhancements and reorganization. meganshand 2015-11-09 14:40:40 -0500
  • 6722ac8e8a Merge pull request #1230 from broadinstitute/rhl_htsjdk_picard_1.141 Ron Levine 2015-11-20 19:47:54 -0500
  • 0b3b09e3ff Move htsjdk & picard to version 1.141 Ron Levine 2015-11-19 20:51:34 -0500
  • dc0e32e3aa Merge pull request #1223 from broadinstitute/rhl_dict_check Ron Levine 2015-11-20 12:43:44 -0500
  • 1443ee8c7f Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1 Mark Fleharty 2015-11-20 11:23:02 -0500
  • ccaddefa19 Validate VCF with sequence dictionary Ron Levine 2015-11-10 14:22:47 -0500
  • 29e86a0d01 Merge pull request #1222 from broadinstitute/yf_percent_informative_read Yossi Farjoun 2015-11-18 10:08:50 -0500
  • 4da0d1300c adding fraction informative reads annotation. Yossi Farjoun 2015-10-29 16:01:47 -0400
  • 2bffe0b428 Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReports_to_protected Eric Banks 2015-11-16 22:26:54 -0500
  • 9d5be24778 Move GatherBqsrReports from private to protected David Roazen 2015-11-10 17:40:58 -0500
  • 2b591d0b6f Merge pull request #1198 from broadinstitute/ldg_moreASannotations ldgauthier 2015-11-10 00:35:15 -0500
  • 25b8ba45f4 More allele-specific annotations: AS_QD and AS_InbreedingCoeff Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918 Also refactored code shared by ExcessHet and InbreedingCoeff Laura Gauthier 2015-10-23 15:23:37 -0400
  • fa6c1c933b Merge pull request #1193 from broadinstitute/vrr_general_independent_af_calculator Valentin Ruano Rubio 2015-11-07 22:14:23 -0500
  • e3d5d96076 Added the AF indepdent calculator for any ploidy but seems that is not doing a good job for haploid vruano 2015-10-09 16:14:41 -0400
  • 49fa06865c Merge pull request #1207 from broadinstitute/mf_SV_bugfix Mark Fleharty 2015-11-06 08:52:38 -0500
  • 8857bc9b3f Resolves issue #1061 to use testid1 rather than testid in two integrationtests. Mark Fleharty 2015-11-05 15:54:35 -0500
  • 975f8a8502 Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_warnings Eric Banks 2015-11-05 16:12:50 -0500
  • 2cc7de4886 Suppress emission of the scary warning message from genotyping to no more than once in anything but DEBUG logging mode. Otherwise it fills up our output logs. Eric Banks 2015-11-05 14:14:47 -0500
  • 448b575701 Merge pull request #1204 from broadinstitute/ms_fix_SelectVariants ldgauthier 2015-11-05 08:07:48 -0500
  • e4627ed5c3 Addressing comments meganshand 2015-11-04 11:00:01 -0500
  • b5165b8d30 Fix for out of date VCF version output meganshand 2015-11-03 17:35:47 -0500
  • 3d1dc303b3 Merge pull request #1197 from broadinstitute/ts_ve_nullPointer ldgauthier 2015-11-02 14:42:50 -0500
  • 33462c7b50 Removed the line that caused a null pointer, as the information it logged was not useful. Updated docs and added an integration test to ensure the code no longer throws the exception. Takuto Sato 2015-10-20 14:49:04 -0400
  • 54ab65a340 Merge pull request #1187 from broadinstitute/ldg_variantEval_famStrat ldgauthier 2015-10-30 08:00:30 -0400
  • f7eb5d3082 Enable family-level stratification (if a ped file is provided) Laura Gauthier 2015-10-22 12:58:24 -0400
  • 4fbcfc2e36 Merge pull request #1173 from broadinstitute/ldg_AS_annotations ldgauthier 2015-10-27 12:04:56 -0400
  • 84006a629b Merge pull request #1190 from broadinstitute/mf_makeRDQHidden Mark Fleharty 2015-10-27 11:59:35 -0400
  • 68a2f1243d Finished draft of code for new map-combine-reduce annotation framework All VQSR annotations can be generated in allele-specific mode Pull out allele-specific annotations in AS_Standard annotation group Laura Gauthier 2015-06-11 10:52:23 -0400
  • 19af5724c5 Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden Mark Fleharty 2015-10-26 14:29:06 -0400
  • fcaf37279c Finished draft of code for new map-combine-reduce annotation framework All VQSR annotations can be generated in allele-specific mode Pull out allele-specific annotations in AS_Standard annotation group Laura Gauthier 2015-06-11 10:52:23 -0400
  • ab247e7570 Merge pull request #1189 from broadinstitute/rhl_laatv_long_allele_choke Ron Levine 2015-10-26 11:02:55 -0400
  • 36ca9fe898 Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window Ron Levine 2015-10-23 20:02:52 -0400
  • 0d936b28c4 Merge pull request #1178 from broadinstitute/ms_ROCCurve meganshand 2015-10-22 09:19:13 -0400
  • aa3087c0d1 Merge pull request #1182 from broadinstitute/rhl_laatv_multiallelic Ron Levine 2015-10-22 08:04:34 -0400
  • 795fe75886 Update doc for multiallelics, trimming is the default behavior Ron Levine 2015-10-16 17:21:52 -0400
  • a57500b2fc ROCCurve High Confidence Mode meganshand 2015-09-29 11:52:09 -0400
  • 7b067c13bd Merge pull request #1176 from broadinstitute/ts_annotateFilterStatus Takuto Sato 2015-10-14 16:17:49 -0400
  • df7a482335 VariantAnnotator now supports annotating FILTER field from an external resource. Updated the docs. Takuto Sato 2015-09-25 15:35:06 -0400
  • 25e0956ebb Merge pull request #1157 from broadinstitute/cn_sample_fix Ron Levine 2015-10-12 13:19:04 -0400
  • e776502c49 Fix Sample mergeValues failure when merging identical string values (#1156). Chris Norman 2015-09-14 19:08:38 -0400
  • 9e168ede3e Merge pull request #1161 from broadinstitute/rhl_va_allele_match Ron Levine 2015-10-08 22:16:01 -0400
  • 2bcded11cb VariantAnnotator checks alleles when annotationg with external resource Ron Levine 2015-09-15 13:19:15 -0400
  • 83e205c27d Merge pull request #1177 from broadinstitute/rhl_rev_1.140 Ron Levine 2015-10-08 15:17:59 -0400
  • 033115eae0 Move htsjdk & picard to version 1.140 Ron Levine 2015-10-08 10:42:05 -0400
  • 173a34a450 Merge pull request #1174 from broadinstitute/eb_fix_combine_for_spanning_dels ldgauthier 2015-10-02 18:02:42 -0400
  • 622ec352bb Fix for combining records in which one has a spanning deletion and needs a padded reference allele. Eric Banks 2015-10-02 14:40:48 -0400
  • 071dbf29dd Merge pull request #1168 from broadinstitute/knoblett Geraldine Van der Auwera 2015-10-01 14:14:07 -0400
  • 506958a0b7 Implemented a new VariantEval evaulation module, MetricsCollection. Fixed null pointer exception, updated tests. Kate Noblett 2015-09-25 13:52:57 -0400
  • e9724ebac7 Merge pull request #1167 from broadinstitute/rhl_bcbs Ron Levine 2015-09-30 10:30:30 -0400
  • 792142ec50 Implement BaseCounts per-sample Ron Levine 2015-09-24 16:23:36 -0400
  • a762dcb6cf Merge pull request #1172 from broadinstitute/ks_jd_parallel_shell kshakir 2015-09-29 20:29:41 -0300
  • 384a09e991 Minor updates to previous ParallelShell commit. Changed `--maximumNumberOfJobsToRunConcurrently`/`-maxConcurrentRun` to `Option[Int]`. Updated licenses. Added basic tests. Removed some IntelliJ warnings. Khalid Shakir 2015-09-28 22:45:50 -0300
  • b045f2d4aa ParallelShell added as a new JobRunner Johan Dahlberg 2015-05-07 15:51:54 +0200
  • 302a69d685 Merge pull request #1165 from broadinstitute/sl_fix_no_calls samuelklee 2015-09-28 12:26:18 -0400
  • 984b1443e8 Merge pull request #1164 from broadinstitute/gg_IntervalCovWithGC_script_1160 Geraldine Van der Auwera 2015-09-25 23:00:21 -0400
  • ed7ff65b2e Merge pull request #1169 from broadinstitute/gvda_typo_fix_#1159 Geraldine Van der Auwera 2015-09-25 22:57:17 -0400
  • 118c559278 Trivial doc typo fix Geraldine Van der Auwera 2015-09-25 18:15:29 -0400
  • c7f76b945e addressing PR comments Samuel Lee 2015-09-24 15:42:51 -0400
  • a5f4b4305b Revived this walker for GP; it does a simple super-fast coverage analysis with GC content and number of dbsnp variants annotated Geraldine Van der Auwera 2015-09-21 02:22:42 -0400
  • 0dacf60012 Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs. Samuel Lee 2015-09-23 14:31:16 -0400
  • ac8b326b92 Merge pull request #1155 from broadinstitute/ms_fix_ignoreAllFilters ldgauthier 2015-09-23 14:11:10 -0400
  • db9aa9cda6 Fix for ignoreAllFilters meganshand 2015-09-11 11:51:09 -0400
  • de97c38a30 Merge pull request #1163 from broadinstitute/ami-fix-typo-ASEReadCounter Eric Banks 2015-09-21 15:46:31 -0400
  • 1ad00cc9d4 fix typo in the ASEReadCounter document Ami Levy Moonshine 2015-09-21 15:30:06 -0400
  • b1cc48da05 Merge pull request #1158 from broadinstitute/ms_HSmetrics meganshand 2015-09-18 13:38:41 -0400
  • cdfe0d7b7c Adding PER_TARGET_COVERAGE option meganshand 2015-09-16 16:02:53 -0400
  • aadf6645f6 Merge pull request #1097 from broadinstitute/rhl_validatevariants_al_cutoff Ron Levine 2015-09-17 14:00:59 -0400
  • 3ecabf7e45 Allow overriding ValidateVariants' hard-coded cutoff for allele length Ron Levine 2015-07-27 09:27:16 -0400
  • 5870225f83 Merge pull request #1153 from broadinstitute/ms_excess_het ldgauthier 2015-09-15 11:52:25 -0400
  • 7e894f3b4c Merge pull request #1148 from broadinstitute/ks_cram_crai kshakir 2015-09-14 23:24:41 -0400
  • 24e24b9468 Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`. Updated other IntelliJ IDEA warnings in GATKBAMIndex. Updated example .cram files to match versions generated by current GATK/HTSJDK. Bumped HTSJDK and Picard to 1.139 releases. Added support for using `-SNAPSHOT` of HTSJDK in the future. Khalid Shakir 2015-08-12 01:23:54 -0300
  • 2507bf8d17 Fixed 7-PL genotypes in InbreedingCoeff tests meganshand 2015-09-14 09:03:17 -0400
  • d767e1722e Excess Het P-value meganshand 2015-09-04 16:41:56 -0400
  • b5cda3e7dc Merge pull request #1154 from broadinstitute/ldg_disableFargoQuery ldgauthier 2015-09-14 11:57:57 -0400
  • 89fc8f04db Disable tests that checks a bam that's moved to Fargo (a.k.a. AWS) Laura Gauthier 2015-09-14 09:29:52 -0400
  • 3db0686dc4 Merge pull request #1133 from broadinstitute/ldg_fixInputPriors ldgauthier 2015-09-12 11:24:31 -0400
  • 53b506a0b8 Make sure inputPriors get used if they are specified Fix usage of AF prior (i.e. theta) in probability of non-reference calculation Refactored duplicate functions Updated docs for heterozygosity Laura Gauthier 2015-08-07 14:56:49 -0400
  • 5fe568c664 Merge pull request #1151 from broadinstitute/rhl_fix_snpmask Ron Levine 2015-09-09 20:50:05 -0400
  • 83a7012d69 Mask snps with --snpmask Ron Levine 2015-09-09 10:37:39 -0400
  • b0dea2ccca Merge pull request #1150 from broadinstitute/eb_keep_iupac_in_IR Eric Banks 2015-09-04 13:43:34 -0400
  • 5f76ae6a37 Don't have the Indel Realigner change IUPAC reference bases. Eric Banks 2015-09-04 11:40:11 -0400
  • cad81a6181 Merge pull request #1149 from broadinstitute/ldg_fixCGPbugForAndrea ldgauthier 2015-09-04 11:17:15 -0400
  • a8851e6763 Merge pull request #1127 from broadinstitute/rhl_hc_qd Ron Levine 2015-09-03 12:21:27 -0400
  • 29ac64f6ce Calculate GenotypeAnnotations before InfoFieldAnnotations Ron Levine 2015-08-07 22:03:22 -0400
  • 4769ef8dad Fix bug when using --ignoreInputSamples Laura Gauthier 2015-09-02 09:27:06 -0400
  • 4464c04c9c Merge pull request #1135 from broadinstitute/sl_issue_1056 samuelklee 2015-08-31 16:09:22 -0400
  • 41256e1405 Added file-extension--dependent interval-list output to RealignerTargetCreator. Samuel Lee 2015-08-12 14:19:04 -0400