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  • 3b8209f3b2 Merge pull request #467 from broadinstitute/rp_fix_names_NA12878ROCCurve Ryan Poplin 2014-01-09 06:56:34 -0800
  • 50cd6781b3 Merge pull request #465 from broadinstitute/eb_improvements_to_ref_confidence_merger MauricioCarneiro 2014-01-08 10:51:01 -0800
  • 8881926bc6 The ROC Curve report lists the name as the name of the vcf file now instead of project+name. Ryan Poplin 2014-01-08 09:44:21 -0500
  • c86e36c909 Merge pull request #466 from broadinstitute/rp_phase3_vqsr_scala Ryan Poplin 2014-01-08 06:39:46 -0800
  • 7d5a710ea6 Adding here the Qscript used to perform the VQSR for 1000 Genomes Project phase 3 Ryan Poplin 2014-01-08 09:38:13 -0500
  • 553b3e56bd Merge pull request #463 from broadinstitute/eb_fix_realigner_bugs_from_pearson Eric Banks 2014-01-08 05:36:11 -0800
  • 0323caefc8 Added some bug fixes to the gVCF merging code after finally getting some real data to play with. Still under construction, awaiting more test data from Valentin. Eric Banks 2014-01-07 15:50:21 -0500
  • f172c349f6 Adding the functionality to enable users to input a file of VCFs for -V. Eric Banks 2014-01-06 16:12:37 -0500
  • c133909d32 Fixed edge condition in the realigner where a realigned read can sometimes get partially aligned off the end of the contig. Eric Banks 2014-01-02 15:35:46 -0500
  • e33d3dafc6 Add documentation for RBP, and also update the MD5 for the tests now that the output uses HP tags instead of '|', which is now reserved for trio-based phasing Menachem Fromer 2014-01-03 12:04:47 -0500
  • d1275651ae Merge remote-tracking branch 'origin/master' into mf_new_RBP Menachem Fromer 2014-01-03 01:13:40 -0500
  • f6a44afa3a Merge pull request #464 from broadinstitute/eb_rev_variant_jar_for_bcf_fixes Eric Banks 2014-01-02 21:05:13 -0800
  • 856c17868b Rev'ing the Variant jar to incorporate some patches to the BCF encoder that Menachem needs. Eric Banks 2014-01-02 23:33:17 -0500
  • 5c32ad174a Merge pull request #452 from broadinstitute/rp_vqsr_aggregate_model Ryan Poplin 2014-01-02 12:54:45 -0800
  • 856c1f87c1 Allow for additional input data to be used in the VQSR for clustering but don't carry it forward into the output VCF file. Ryan Poplin 2013-12-11 14:43:07 -0500
  • c82501ac35 Merge pull request #462 from broadinstitute/rp_SingleSampleHC_exome_scala Ryan Poplin 2014-01-02 08:57:27 -0800
  • 15372c4873 Adding SingleSampleHC_exome.scala for Valentin to use as a jumping off point. Ryan Poplin 2014-01-02 11:56:17 -0500
  • f81a38f596 Merge pull request #446 from broadinstitute/ami-RNAseq-tools amilev 2014-01-01 21:06:25 -0800
  • 1223345726 Merge pull request #459 from broadinstitute/eb_fix_bad_hmm_clipping MauricioCarneiro 2014-01-01 20:00:34 -0800
  • 6da53aea09 Write a new tool for spliting reads that have N cigar string. For example, this tool can be used for processing bowtie RNA-seq data. Each read with k N-cigar elemments is plit to k+1 reads. The split is done by hard clipping the bases rest of the bases. Ami Levy-Moonshine 2013-11-14 13:09:38 -0500
  • bb4c4b1fcd Fixed up edge condition for clipping long reads in the HMM. MD5s change because some reads were incorrectly getting clipped before. Eric Banks 2014-01-01 00:34:11 -0500
  • ece346689c Merge pull request #460 from broadinstitute/mc_document_readclippingstats Eric Banks 2014-01-01 16:00:40 -0800
  • 154bab0849 Merge pull request #461 from broadinstitute/mc_make_comparebams_private Eric Banks 2014-01-01 15:58:05 -0800
  • d52bd44867 Move CompareBAMs to private Mauricio Carneiro 2014-01-01 14:33:23 -0500
  • d1febb89c8 Better documentation for ReadClippingStats walker Mauricio Carneiro 2014-01-01 14:26:26 -0500
  • 9355598129 Merge pull request #458 from broadinstitute/eb_dont_fail_when_using_incompatible_annotation Eric Banks 2013-12-31 21:22:26 -0800
  • 050ca8ae09 Merge pull request #457 from broadinstitute/eb_rev_variant_for_doc_updates Eric Banks 2013-12-31 20:49:20 -0800
  • 9665f75ad4 Don't fail in annotations if the wrong tools are calling them, just silently skip them. This is important for cases when users want to use annotation groups (like all experimental annotations). Eric Banks 2013-12-31 23:45:21 -0500
  • f82a7c3f4c Updating variant jar. Eric Banks 2013-12-31 13:23:11 -0500
  • 5a1564d1f2 Merge pull request #456 from broadinstitute/eb_unify_hc_combination_steps Eric Banks 2013-12-31 18:57:27 -0800
  • 83e09b1f64 Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. Eric Banks 2013-12-08 01:03:46 -0500
  • 9394af1230 Merge pull request #454 from jsilter/master Eric Banks 2013-12-19 08:47:24 -0800
  • 48ef7a1a2f Merge remote-tracking branch 'origin/master' into mf_new_RBP Menachem Fromer 2013-12-19 10:42:20 -0500
  • 26a7082018 Merge pull request #455 from broadinstitute/dr_add_min_max_argument_values Eric Banks 2013-12-18 20:40:06 -0800
  • 4a79831adc Add ability to specify min/max required/recommended values for numeric arguments in the @Argument annotation David Roazen 2013-12-18 14:53:57 -0500
  • 0c7ea2d823 Add label and specVersion fields to MongoDBManager.Locator Jacob Silterra 2013-12-18 17:21:53 -0500
  • d32c900018 Merge pull request #453 from broadinstitute/eb_rev_variant_for_validation_bug Eric Banks 2013-12-18 11:13:11 -0800
  • 265cb3eb5b Updated the variant jar to grab a bug fix that I made to it Eric Banks 2013-12-17 11:52:34 -0500
  • 5ed627d448 Merge pull request #450 from broadinstitute/vrr_graphLikelihoods_fix250PCRFree Valentin Ruano Rubio 2013-12-13 09:22:46 -0800
  • 5db520c6fa Fixed issue > 0 log likelihoods using GraphBased likelihood engine reported by Mauricio Valentin Ruano-Rubio 2013-12-09 08:18:56 -0500
  • 3e8feff429 Merge pull request #451 from broadinstitute/jt_mongo_migration Eric Banks 2013-12-13 07:40:35 -0800
  • 58217a5c4b Move the SelectVariantsFromMongo helper classes to archive Joel Thibault 2013-12-12 18:50:10 -0500
  • d6169a28cd Merge pull request #448 from broadinstitute/eb_add_stuff_to_the_bundle Bertrand 2013-12-12 07:31:59 -0800
  • 400e7c1404 Fixed bug in the filtering of lifted over variants where a deletion at the end of a contig could cause it to error out. Added a unit test. Eric Banks 2013-12-07 22:07:22 -0500
  • ab33db625f Merge pull request #449 from broadinstitute/eb_move_calc_posteriors_to_protected Eric Banks 2013-12-07 22:18:46 -0800
  • f1970b923e Moved CalculatePosteriors from private to protected, in preparation for 3.0. Renamed it CalculateGenotypePosteriors. Also, moved the utility code to a proper utility class instead of where Chris left it. No actual code modifications made in this commit. Eric Banks 2013-12-08 00:00:23 -0500
  • 418fbdfbab Added HC trio calls and NA12878 KB snapshot to resource bundle. Also, don't touch the current link until the resources are finished being produced. Eric Banks 2013-12-07 21:03:27 -0500
  • 932cd3ada7 Fix 3rd-party library dependency issues in the HC/PairHMM tests David Roazen 2013-12-06 13:16:55 -0500
  • 70e2d21e12 Merge remote-tracking branch 'unstable/master' Eric Banks 2013-12-06 11:45:12 -0500
  • 7ed5344f8b Merge pull request #447 from broadinstitute/dr_segregate_kb_tests Eric Banks 2013-12-06 08:43:07 -0800
  • 10dc038a24 Separate tests that access the knowledge base from other tests David Roazen 2013-12-05 17:31:32 -0500
  • 1a0e140ab5 Merge pull request #445 from broadinstitute/dr_rev_picard_for_2.8 Eric Banks 2013-12-05 15:03:27 -0800
  • 32cca883fc Merge pull request #444 from broadinstitute/dr_parallel_test_runner_adjustments Eric Banks 2013-12-05 15:02:39 -0800
  • 47ea3c3b22 Tweak parallel test runner in attempt to decrease spurious failures David Roazen 2013-12-05 13:49:37 -0500
  • 0e65296efb Rev picard, sam-jdk, tribble, and variant jars to 1.104.1628 David Roazen 2013-12-05 12:25:33 -0500
  • 6d2fcd2df9 Merge pull request #443 from broadinstitute/eb_better_doc_for_minpruning Eric Banks 2013-12-05 08:52:56 -0800
  • e022db4690 Added docs for the minPruning argument in the HC Eric Banks 2013-12-05 11:50:56 -0500
  • 623aaa0d6f Merge pull request #442 from broadinstitute/gg_fixdoc_deletions Eric Banks 2013-12-04 17:37:18 -0800
  • 3ab2f4edb2 Fixed documentation for -deletions argument in the UAC Geraldine Van der Auwera 2013-12-04 19:55:24 -0500
  • 0d94019bd6 Merge pull request #434 from broadinstitute/mc_dt_gccontent amilev 2013-12-04 09:42:26 -0800
  • 41a0aecb07 Merge pull request #441 from broadinstitute/jt_gvcf_idx_user_error Eric Banks 2013-12-03 21:54:11 -0800
  • 5fe0531b4d Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy Joel Thibault 2013-12-03 16:36:23 -0500
  • 8571a641bf Add @Advanced to variant_index_type and variant_index_parameter Joel Thibault 2013-12-03 16:40:31 -0500
  • 701ede2817 Add GC Content to DiagnoseTargets Mauricio Carneiro 2013-11-27 11:53:49 -0500
  • 61b50a02b1 Merge pull request #431 from broadinstitute/jt_custom_vcf_idx droazen 2013-12-03 19:32:36 -0800
  • fd0a02e52e New VCF engine arguments to specify an alternate IndexCreator - CatVariants updates to use custom VCF indices - Scala scripts for VCF index testing Joel Thibault 2013-11-07 11:49:13 -0500
  • 42f78bdb3a Add a class-based DataProvider Joel Thibault 2013-11-27 11:45:58 -0500
  • cd3ee2ae7e whitespace Joel Thibault 2013-11-15 16:50:26 -0500
  • ed6f069191 Rev Picard 1.102.1595 Joel Thibault 2013-11-13 15:31:41 -0500
  • d90b295570 Merge pull request #440 from broadinstitute/eb_selection_should_keep_pls Eric Banks 2013-12-03 07:08:01 -0800
  • cb2f228f5a Archiving SelectVariantsFromMongo since it has started to diverge from SelectVariants Eric Banks 2013-12-02 12:49:31 -0500
  • 6bee6a1b53 Change the behavior of SelectVariants for PL/AD when it encounters a record that has lost one or more alternate alleles. Eric Banks 2013-12-02 12:46:51 -0500
  • b1073fb17b Merge pull request #439 from broadinstitute/vrr_graphLikelihoods2 Valentin Ruano Rubio 2013-12-02 18:54:15 -0800
  • 0f99778a59 Adding Graph-based likelihood ratio calculation to HC Valentin Ruano-Rubio 2013-11-18 12:07:59 -0500
  • 00116609e4 Archive addition as a result of the work on adding Graph-based likelihood ratio calculation to HC. Valentin Ruano-Rubio 2013-11-18 12:05:42 -0500
  • 84ddfb41b5 Merge pull request #438 from broadinstitute/rp_vqsr_num_bad_stability_fixes_and_runtime_optimizations Eric Banks 2013-12-02 08:37:37 -0800
  • 6a922e7aca Merge pull request #435 from broadinstitute/eb_fix_ug_bug_for_long_deletions Ryan Poplin 2013-12-02 08:09:23 -0800
  • b57054c63c Various VQSR optimizations in both runtime and accuracy. Ryan Poplin 2013-09-30 11:14:35 -0400
  • 6d43952ccc Merge pull request #436 from broadinstitute/eb_fix_mq_byte_issue_in_RR Eric Banks 2013-11-27 19:25:36 -0800
  • df6499e58c Bug fix for RR: stop (incorrectly) pulling the MQ out of the SAMRecord as a byte instead of an int. Eric Banks 2013-11-27 15:53:11 -0500
  • 51d1a26725 Bug fix for something Guillermo added to UG before he left to support calling indels from reduced reads. Eric Banks 2013-11-26 22:36:35 -0500
  • 42bf83cdc8 Merge pull request #433 from broadinstitute/eb_finish_chartl_likelihood_posteriors Eric Banks 2013-11-27 10:53:05 -0800
  • 1f777c4898 Introducing the latest-and-greatest in genotyping: CalculatePosteriors. Chris Hartl 2013-11-21 02:49:38 -0500
  • 6d0d555925 Merge pull request #432 from broadinstitute/gg_fixSplitSamFile Eric Banks 2013-11-26 13:01:22 -0800
  • 429582589f Set SAMFileWriter to create index in ReadUtils to fix SplitSamFile issue Geraldine Van der Auwera 2013-11-26 15:53:29 -0500
  • 5da901a8b1 Merge pull request #430 from broadinstitute/gg_patch_queueextensions Eric Banks 2013-11-25 08:09:42 -0800
  • abf70dc071 Merge pull request #428 from broadinstitute/eb_various_HC_bug_fixes Ryan Poplin 2013-11-25 06:36:31 -0800
  • 25bc6e64ae Patched Queue extensions lacking a main class definition Geraldine Van der Auwera 2013-11-22 14:47:53 -0500
  • 0fac4fb3b6 Make the reference model calculation work with reduced reads. Eric Banks 2013-11-21 10:21:25 -0500
  • adb77b406f Fixed poor implementation of isRefSource() and isRefSink() among others. Eric Banks 2013-11-20 15:49:54 -0500
  • b5f3bf5f06 Merge pull request #427 from broadinstitute/gg_update_gatkdocs_template Eric Banks 2013-11-19 17:59:08 -0800
  • b42ccdce11 Tweaked gatkdocs index template Geraldine Van der Auwera 2013-11-19 15:05:41 -0500
  • b603e6674d Merge pull request #425 from broadinstitute/ami_moleculo_project_changes amilev 2013-11-18 14:33:49 -0800
  • e6ef37de1d Add an option to filter the read bases that are taking into account for the coveraged intervals. For that, new two arguments were added: minBaseQuality and minMappingQuality Ami Levy-Moonshine 2013-11-07 17:16:14 -0500
  • 6ad841cec5 Rewrite ReadLengthDistribution to count the read lengths into a hash table first and only at the end to produce a GATK report table. Before that fix, the tool was couldn't work with more then one RG before. - Address all review comments Ami Levy-Moonshine 2013-11-07 14:54:35 -0500
  • cc85e373d0 Merge pull request #426 from broadinstitute/ami_fix_MoleculoPipeline_suffix_bug amilev 2013-11-18 08:55:46 -0800
  • 9c1023c933 fix a (ugly) weird error from last commit that changed all the scala files to end with MoleculoPipeline.scala Ami Levy-Moonshine 2013-11-18 11:44:24 -0500
  • 6448cc53f5 Merge pull request #422 from broadinstitute/ami-NPE-fix-NA12878 amilev 2013-11-14 12:06:16 -0800
  • 2ff0c23b53 fix missed NPE error in AssessNA12878. Add a check and an clear error message. add unitTest for that case (when a file has genotypes but does not NA12878 as a sample) Ami Levy-Moonshine 2013-11-12 12:00:53 -0500
  • 7f08250870 Merge pull request #417 from broadinstitute/bt_pairhmm_api_cleanup2 MauricioCarneiro 2013-11-14 10:47:07 -0800