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  • bf5ce41321 Merge pull request #336 from broadinstitute/gda_ancient_dna_pls Eric Banks 2013-07-18 10:47:52 -0700
  • 9dd109b79a Last feature request from Reich/Paavo labs: the allSitePLs feature in UG worked but not quite filled requirements. What's needed is the ability to have all 10 PLs for EVERY site, regardless of whether they are variant or not. Previous version only emitted the 10 PLs in reference sites. Problem is that, if all PLs are emitted in all sites and every single site is quad-allelic (only way to have the PLs printed out in a valid way) then the ability to filter variants and to use the INFO fields may be compromised. So, compromise solution is to go back to having biallelic PLs but emit a new FORMAT field, called APL, which has the 10 values, but all other statistics and regular PLs are computed as before. Note that integration test had to be disabled, as the BCF2 codec apparently doesn't support writing into genotype fields other than PL,DP,AD,GQ,FT and GT. Guillermo del Angel 2013-07-16 11:14:48 -0400
  • 234f564009 Merge pull request #335 from broadinstitute/eb_improvements_to_KB_assessment Eric Banks 2013-07-18 08:47:03 -0700
  • 5d1454c6b0 Several improvements to the NA12878 knowledge base. Eric Banks 2013-07-12 11:46:34 -0400
  • 6440f926d3 Parallel tests: use /broad/hptmp as working dir instead of /broad/classA-test David Roazen 2013-07-15 15:12:31 -0400
  • f2fca40b2b Merge pull request #333 from broadinstitute/dr_fix_SAMReaderID_hashing Eric Banks 2013-07-15 12:20:50 -0700
  • 28b8815688 Merge pull request #301 from broadinstitute/mc_tsca_project chartl 2013-07-15 11:21:41 -0700
  • c15751e41e SAMReaderID: fix bug with hash code and equals() method David Roazen 2013-07-15 13:28:07 -0400
  • 51b95589e5 Merge pull request #331 from broadinstitute/gda_pool_caller_paper Eric Banks 2013-07-15 09:06:14 -0700
  • 464cf33dd3 Committing pool caller script changes for posterity: mostly updating the reference sample calls to latest gold standard, adding filtering tweaks and redo of R scripts. Guillermo del Angel 2013-06-19 13:27:12 -0400
  • 5d198d3400 Added write to likelihoods.txt for batch hmm Scott Thibault 2013-07-15 10:16:39 -0500
  • 3459eab413 Barcodes per Amplicon count tool Mauricio Carneiro 2013-06-10 13:28:12 -0400
  • 0a8f75b953 Merge branch 'master' into st_fpga_hmm sathibault 2013-07-15 08:17:32 -0500
  • 1575fdaab4 Merge pull request #330 from broadinstitute/yf_adding_per_sample_allele_biased_downsampling_to_HC Eric Banks 2013-07-13 18:50:32 -0700
  • 8c07614321 QualifyMissingIntervals: support different formats Mauricio Carneiro 2013-07-10 16:16:28 -0400
  • afcf7b96db - Added per-sample AlleleBiasedDownsampling capability to HaplotypeCaller - Added integration test to show that providing a contamination value and providing same value via a file results in the same VCF Yossi Farjoun 2013-07-10 08:06:54 -0400
  • 7ddf85c040 Merge pull request #329 from broadinstitute/eb_more_sensitivity_improvements_to_the_HC delangel 2013-07-12 10:37:43 -0700
  • b16c7ce050 A whole slew of improvements to the Haplotype Caller and related code. Eric Banks 2013-06-28 07:41:06 -0400
  • 3e1a96844b Merge pull request #328 from broadinstitute/dr_dependency_analyzer_output_loader Eric Banks 2013-07-11 20:31:17 -0700
  • 8ef4e6c9f7 DependencyAnalyzerOutputLoader: allows output from the dependency analyzer to be loaded and queried David Roazen 2013-07-11 14:55:05 -0400
  • 23fe3e449a Revert "Fixed batching bug." sathibault 2013-07-11 11:30:37 -0500
  • 7458b59bb3 Fixed batching bug. sathibault 2013-07-11 11:08:46 -0500
  • ccc0ee5b4d Merge pull request #327 from broadinstitute/gda_large_indel_improvement Eric Banks 2013-07-11 06:58:13 -0700
  • a8ea57df9e Merge branch 'master' of github.com:broadinstitute/gsa-unstable Menachem Fromer 2013-07-10 16:44:35 -0400
  • aba55dbb23 Moved some HC parameters related to active region extensions to command line arguments so that they're more easily modified. Some of these parameters need tinkering in order to call some large indels. See GSA-891 and subtasks for particular examples thereof. Guillermo del Angel 2013-07-10 14:29:13 -0400
  • 2d81234ed8 Merge pull request #326 from broadinstitute/dr_dependency_analyzer_add_manual_dependencies droazen 2013-07-09 10:12:50 -0700
  • de06eda6ac Dependency analyzer improvements David Roazen 2013-07-08 14:27:58 -0400
  • 5dbb582be7 Merge pull request #310 from broadinstitute/mc_interval_list_to_fastq Eric Banks 2013-07-08 14:30:43 -0700
  • ac77a4c699 Merge pull request #316 from broadinstitute/md_filter_counting Valentin Ruano Rubio 2013-07-08 10:58:47 -0700
  • 380a01ddc0 Merge pull request #322 from broadinstitute/eb_add_review_indexes_to_repo Eric Banks 2013-07-08 10:15:46 -0700
  • 4fe26ea2cf Merge pull request #323 from broadinstitute/eb_fix_sorting_in_reduce_reads Eric Banks 2013-07-08 10:15:28 -0700
  • c5a2a8f39f Merge pull request #324 from broadinstitute/eb_AnalyzeCovariates_is_not_deprecated Eric Banks 2013-07-08 10:15:10 -0700
  • bc28a1f236 pipeline test runner: create temp dir if it doesn't exist David Roazen 2013-07-08 12:34:20 -0400
  • 1c28bd2ffd Merge pull request #325 from broadinstitute/dr_general_calling_pipeline_walker_list Ryan Poplin 2013-07-08 09:28:13 -0700
  • 46b453a69d List of walkers used by the GeneralCallingPipeline David Roazen 2013-07-08 11:53:58 -0400
  • 73fc7f6ab1 Reduce Reads output should never be expected to be sorted (hence the need to sort on disk) but for some reason it was with -nwayout mode. Eric Banks 2013-07-08 10:33:36 -0400
  • 921f551426 AnalyzeCovariates is no longer a deprecated tool. Eric Banks 2013-07-08 09:48:12 -0400
  • 3e357ac8cf It was annoying me that these index files kept showing up in 'git status' Eric Banks 2013-07-08 09:46:08 -0400
  • 0aa9d02570 Merge pull request #321 from broadinstitute/eb_fix_annotating_multiple_comps Mark DePristo 2013-07-05 05:05:09 -0700
  • 5f5c90e65c Fix bug introduced recently in the VariantAnnotator where only the last -comp was being annotated at a site. Eric Banks 2013-07-05 00:04:52 -0400
  • 6d69c7dc71 Disable RetryMemoryLimit pipeline test David Roazen 2013-07-03 13:38:28 -0400
  • 8d00e558fb Merge pull request #317 from broadinstitute/dr_dependency_analyzer Tadeusz Jordan 2013-07-03 08:46:37 -0700
  • 7cdb7ac572 Merge pull request #320 from broadinstitute/gg_cleanup_licenses_PT51255639 Mark DePristo 2013-07-03 04:55:15 -0700
  • d55dddfdba deleted old license files Geraldine Van der Auwera 2013-07-02 16:36:47 -0400
  • 3db02e5ef1 Merge pull request #315 from broadinstitute/md_ref_conf_hc Mark DePristo 2013-07-02 13:04:33 -0700
  • 2e87d09c26 Merge pull request #319 from broadinstitute/dr_packaging_system_fail_gracefully_when_bcel_not_installed droazen 2013-07-02 13:01:45 -0700
  • 75d1f64416 Fail gracefully in the packaging system when bcel is not installed David Roazen 2013-07-02 15:46:34 -0400
  • 35cdc16822 Merge pull request #318 from broadinstitute/dr_improve_dcov_documentation Mark DePristo 2013-07-02 12:47:29 -0700
  • 5f34054cc1 Remove filtering of MAPQ 0 reads from CalledHaplotypeBAMWriter Mark DePristo 2013-07-01 14:55:15 -0400
  • 7be01777f6 Bugfix for incPos in GenomeLoc Mark DePristo 2013-07-01 14:51:15 -0400
  • ed0b1c5aba Fix bug in ReadThreadingAssembler in cycle failures causing NPE Mark DePristo 2013-06-25 10:53:33 -0400
  • e3e8631ff5 Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences Mark DePristo 2013-06-19 15:07:35 -0400
  • 41aba491c0 Critical bugfix for adapter clipping in HaplotypeCaller Mark DePristo 2013-06-27 15:44:53 -0400
  • cdea744b95 Improve -dcov documentation to address recent user confusion David Roazen 2013-07-02 15:27:36 -0400
  • 8eab59419d Ant-based walker dependency analyzer David Roazen 2013-06-25 15:18:47 -0400
  • 9df58314ab Bugfix for counting of applied filters Mark DePristo 2013-07-01 21:09:48 -0400
  • c3d59d890d Update licenses for new PbsEngine* classes David Roazen 2013-07-01 15:50:20 -0400
  • 2964ebaa4e Merge pull request #314 from broadinstitute/ks_francesco_pbs_patch droazen 2013-07-01 12:39:38 -0700
  • f0c36e2890 Fixing failed test for HSP by changing dcov from 60 to 200. Khalid Shakir 2013-07-01 11:39:18 -0400
  • ec206eccfc Switch "all" test pipeline job runners to mean the job runners that run at The Broad. Khalid Shakir 2013-06-27 15:07:59 -0400
  • acf90ca027 corrected number of arguments passed to PbsEngineJobRunner when requesting multiple cores Francesco 2013-06-27 11:08:59 +0200
  • 948b2fca20 added PbsEngine plugin into engine folders, to be called in Queue with -jobRunner PbsEngine; the plugin is written modifying the existing GridEngine plugin, used as a template Francesco 2013-06-26 10:29:45 +0200
  • 4ec50caea2 Merge pull request #313 from broadinstitute/mc_generalize_dt_scala_script Mark DePristo 2013-06-29 11:00:00 -0700
  • a6b569b395 Added all the parameters to the scala script for DiagnoseTargets Mauricio Carneiro 2013-06-25 15:17:40 -0400
  • 815f119f7c Walker to create a fastq file from an interval list Mauricio Carneiro 2013-06-26 23:51:22 -0400
  • 31827022db Fix pipeline tests that were not respecting the pipeline test dry run setting David Roazen 2013-06-28 14:57:16 -0400
  • 82dcdc01c0 Merge branch 'master' into st_fpga_hmm Scott Thibault 2013-06-28 10:13:05 -0500
  • e691fa3e19 FPGA null pointer bug fix Scott Thibault 2013-06-28 08:52:09 -0500
  • 1ec56c9e64 Merge pull request #311 from broadinstitute/eb_require_min_mq_for_FN_in_kb Ryan Poplin 2013-06-27 16:49:45 -0700
  • 5717f3dc1c Merge pull request #312 from broadinstitute/eb_fix_assessna12878_and_add_integration_tests Mark DePristo 2013-06-27 13:51:37 -0700
  • 7aa1f56dff We need to enforce a minimum base and mapping quality threshold to penalize a callset for FNs. Eric Banks 2013-06-27 10:47:05 -0400
  • 1f1da56d28 I allowed a bad push yesterday with the KB because there weren't any integration tests for the assessment. Eric Banks 2013-06-27 15:40:19 -0400
  • 825b603acb Merge pull request #298 from broadinstitute/md_likelihood_rank_sum Ryan Poplin 2013-06-27 11:14:25 -0700
  • de7fe2e086 Merge pull request #308 from broadinstitute/rp_assessment_low_coverage Mark DePristo 2013-06-27 06:46:23 -0700
  • 9f08718636 Merge pull request #309 from jsilter/master Eric Banks 2013-06-26 16:00:51 -0700
  • beb834e849 Add "isComplexEvent" as attribute to VariantContextBuilder for MongoVariantContext Jacob Silterra 2013-06-26 17:12:32 -0400
  • fe5348ea5d Don't count no coverage sites as false negatives in the assessment against the knowledge base Ryan Poplin 2013-06-26 16:02:44 -0400
  • a514dd0643 Merge pull request #307 from broadinstitute/eb_rr_off_by_one_error Mark DePristo 2013-06-26 13:02:23 -0700
  • 876e40466a Proper fix for previous RR -cancer_mode fix. Eric Banks 2013-06-26 14:48:09 -0400
  • 95eab80f9b Merge pull request #306 from broadinstitute/eb_make_assessreducedquals_hidden Eric Banks 2013-06-26 08:47:28 -0700
  • f242be12c0 Make this walker @Hidden Eric Banks 2013-06-26 11:45:21 -0400
  • 28d4c3debc Merge pull request #305 from broadinstitute/dr_move_DownsampleReadsQC_to_private Mark DePristo 2013-06-25 16:33:20 -0700
  • 94294ed6c4 Move DownsampleReadsQC walker to private David Roazen 2013-06-25 15:48:44 -0400
  • d13ed06e9d Merge pull request #303 from broadinstitute/eb_update_kb_to_use_exome_intervals Mark DePristo 2013-06-24 13:06:52 -0700
  • 6dc816beee Various updates to have the KB use the expanded exome intervals (from D MacArthur) in addition to chr20. Eric Banks 2013-06-17 13:21:21 -0400
  • ff76d0c877 Merge pull request #304 from broadinstitute/eb_rr_header_negative_fix_again Mark DePristo 2013-06-24 11:55:52 -0700
  • 165b936fcd Fixing the 'header is negative' problem in Reduce Reads... again. Eric Banks 2013-06-24 14:06:21 -0400
  • b97f9a487d Merged bug fix from Stable into Unstable Valentin Ruano-Rubio 2013-06-24 14:00:01 -0400
  • 521d9c1df5 Merge pull request #302 from broadinstitute/mc_processing_pipeline2 Mark DePristo 2013-06-24 09:52:55 -0700
  • c38b8065d8 quick fixes to the scala script Mauricio Carneiro 2013-04-25 20:13:20 -0400
  • 191e4ca251 Merge pull request #300 from broadinstitute/mc_move_qualify_intervals_to_protected Mark DePristo 2013-06-24 09:35:45 -0700
  • d8ca4d3e6d Merge pull request #299 from broadinstitute/eb_mate_fixer_confused_by_nonprimary_alignment Yossi Farjoun 2013-06-24 06:58:27 -0700
  • 3e5ff6095f Added the pertinent DocumentedGATKFeature annotation ot AnalyzeCovariates Valentin Ruano-Rubio 2013-06-21 17:02:26 -0400
  • d976aae2b1 Another fix for the Indel Realigner that arises because of secondary alignments. Eric Banks 2013-06-21 16:59:22 -0400
  • 8caf39cb65 Experimental LikelihoodRankSum annotation Mark DePristo 2013-06-20 12:57:14 -0400
  • f726d8130a VariantRecalibrator bugfix for bad log10sumlog10 values Mark DePristo 2013-06-20 15:15:17 -0400
  • dee51c4189 Error out when NCT and BAMOUT are used with the HaplotypeCaller Mark DePristo 2013-06-21 09:25:57 -0400
  • e03a5e9486 Update source release script in attempt to work around intermittent github issues David Roazen 2013-06-20 16:43:59 -0400
  • 0018af0c0a Update README file for the 2.6 release David Roazen 2013-06-20 13:08:29 -0400
  • 6977d6e2a7 Merge remote-tracking branch 'unstable/master' Eric Banks 2013-06-20 12:14:33 -0400