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  • ee5de8510d Merge pull request #380 from broadinstitute/gg_gatkdocs_arglabels droazen 2013-08-16 15:34:56 -0700
  • 80ed186971 More detailed labels for arguments in the gakdocs (requested by David) Geraldine Van der Auwera 2013-08-16 14:25:53 -0400
  • 6cda283115 Merge pull request #378 from broadinstitute/gg_mutehelp Geraldine Van der Auwera 2013-08-16 10:11:28 -0700
  • 9bb0aac7bf Disabled the help system's printout of cmdline options when GATK errors out. Now the user has to explicitly ask for it using -h. Geraldine Van der Auwera 2013-08-16 12:09:09 -0400
  • 3841635fcb Changed 'depreciated' to the more correct 'deprecated' Geraldine Van der Auwera 2013-08-16 13:06:41 -0400
  • a21d5252c8 Merge pull request #377 from broadinstitute/eb_experiment_with_pcr_error_model Ryan Poplin 2013-08-16 08:38:55 -0700
  • 08be871309 Removing unused code in VariantsToTable: GQ is not an INFO field and is taken care of by -GF and not -F. Eric Banks 2013-08-13 15:27:17 -0400
  • 17eb7b49fe Adding ability to use Ryan's PCR error modeling to the Haplotype Caller. Eric Banks 2013-08-12 13:08:55 -0400
  • e7152e10f7 Rev'ing picard, tribble, and variant jars. Eric Banks 2013-08-16 00:13:40 -0400
  • 07f3f6f69d Some minor updates to the KB: Eric Banks 2013-08-12 10:58:53 -0400
  • 1a5e4cc4e7 Merge pull request #375 from broadinstitute/rp_queue_jobreport_rscript Eric Banks 2013-08-14 12:48:42 -0700
  • 7f48f991cc Merge pull request #376 from broadinstitute/gg_AR_gatkdocfix Eric Banks 2013-08-14 12:48:05 -0700
  • 19a4bf9ff0 made AR an Advanced argument to discourage basic users from fiddling with it Geraldine Van der Auwera 2013-08-14 14:46:17 -0400
  • d4ac183580 Something changed with the ggtitle syntax in the latest version of ggplot2. Ryan Poplin 2013-08-14 14:40:03 -0400
  • 928a9779db Merge pull request #374 from broadinstitute/mc_dpp_updates Eric Banks 2013-08-14 04:50:25 -0700
  • 765f5450ac Updated Full Processing Pipeline Mauricio Carneiro 2013-07-25 17:34:53 -0400
  • 69e78efeae Merge pull request #366 from broadinstitute/gg_gatkdocfixes Eric Banks 2013-08-13 04:52:03 -0700
  • bcf9a1cda5 Merge pull request #370 from broadinstitute/rp_dont_output_filtered_variants_in_VQSR Eric Banks 2013-08-12 12:01:50 -0700
  • 4aeb37e1e7 Merge pull request #373 from broadinstitute/rp_vqsr_numbad_docs Eric Banks 2013-08-12 10:56:46 -0700
  • a45011d7e7 Adding mode to VQSR to not output variant records that are filtered out after applying the recalibration. Necessary for 1000G calling. Ryan Poplin 2013-08-08 15:39:30 -0400
  • 59f56bef30 Cleaning up help text for the -numBad argument. Ryan Poplin 2013-08-12 09:45:41 -0400
  • 163d796ae7 Merge pull request #372 from broadinstitute/eb_add_zook_reviews_to_script Eric Banks 2013-08-12 06:51:31 -0700
  • b86742903b Forgot to add this in the previous commit to add J Zook's reviews Eric Banks 2013-08-12 09:50:41 -0400
  • a2134a92fb Merge pull request #371 from broadinstitute/eb_add_zook_reviews Eric Banks 2013-08-12 06:45:11 -0700
  • 8071862af8 Adding Justin Zook's review file to the KB Eric Banks 2013-08-12 09:37:46 -0400
  • a09831489b Disabled emission of doc URLs for external codecs to avoid broken links Geraldine Van der Auwera 2013-08-06 16:45:11 -0400
  • 4d20c71e09 Improvements to various gatkdocs Geraldine Van der Auwera 2013-08-06 13:03:33 -0400
  • 8b5178bd59 Merge pull request #368 from broadinstitute/md_incremental_caller Mark DePristo 2013-08-09 08:21:03 -0700
  • 415aee2be2 Two scripts to enable assessment of the value of joint calling and the effectiveness of the joint caller Mark DePristo 2013-07-18 08:23:44 -0400
  • b7d1096ced Added onlyEmitSamples argument to UnifiedGenotyper Mark DePristo 2013-07-30 09:26:18 -0400
  • cf5dd58303 Merge pull request #369 from broadinstitute/eb_small_updates_to_kb Ryan Poplin 2013-08-09 06:09:27 -0700
  • dd85646067 Various small improvements to the KB assessments. Eric Banks 2013-08-08 15:13:16 -0400
  • ccf0df0fea Misc. debugging functionality to FS calculation (disabled by default) Mark DePristo 2013-07-24 11:40:28 -0400
  • 1f86cf13d1 Merge pull request #359 from lbergelson/lb_relax_add_parameter kshakir 2013-08-07 06:45:01 -0700
  • 6d67795916 Merge pull request #365 from broadinstitute/md_kb_improvements Eric Banks 2013-08-07 06:38:21 -0700
  • 66e1b75118 Critical bugfix for OneChunkIterator Mark DePristo 2013-08-01 08:11:11 -0400
  • 7aba5a2f9f Several improvements to AssessNA12878 and KB Mark DePristo 2013-07-19 08:45:48 -0400
  • 00f4d767e4 Merge pull request #364 from broadinstitute/md_vqsr_improvements Mark DePristo 2013-08-07 04:37:45 -0700
  • c21402d4af Separate num Gaussians for + and - GMM in VQSR Mark DePristo 2013-08-05 14:52:53 -0400
  • 44348a3761 Merge pull request #363 from broadinstitute/md_het_docs Mark DePristo 2013-08-07 04:28:16 -0700
  • 318f7e74e4 Better docs on the meaning of heterozygosity Mark DePristo 2013-07-24 08:44:51 -0400
  • dd0e6409c6 Merge pull request #367 from broadinstitute/md_hc_ref_fix Eric Banks 2013-08-06 20:37:08 -0700
  • 40bc7d6a9c Bugfix for ReferenceConfidenceModel Mark DePristo 2013-08-06 15:51:57 -0400
  • 6dfd17122f Merge pull request #362 from broadinstitute/rp_single_sample_hc_pipeline Ryan Poplin 2013-08-06 12:11:50 -0700
  • ee0aba224c Adding single sample HC qscript for Mauricio. Ryan Poplin 2013-08-06 15:09:56 -0400
  • 81a74351fd Merge pull request #360 from broadinstitute/rp_vqsr_ordering_of_annotations_bug Mark DePristo 2013-08-03 09:49:42 -0700
  • a46f633bd6 Fix for the VQSR visualization script with the new ordering of annotations. Ryan Poplin 2013-08-02 19:10:45 -0400
  • af36c7ce9a Update QScript.scala lbergelson 2013-08-02 14:05:27 -0400
  • 08a7ef6620 Merge pull request #358 from broadinstitute/md_tribble_reuse_query_stream Eric Banks 2013-08-02 10:29:39 -0700
  • d5dd3b23db Rev picard to get optimized tribble feature reads Mark DePristo 2013-08-02 09:16:50 -0400
  • 9316a70d1e Merge pull request #355 from broadinstitute/eb_add_error_handling_to_kb jmthibault79 2013-08-02 06:40:41 -0700
  • ae5fc4c726 Merge pull request #356 from broadinstitute/mc_refbias Eric Banks 2013-08-02 06:30:56 -0700
  • 8a1e2d58ef Merge pull request #357 from broadinstitute/mc_resort_haplotypes Eric Banks 2013-08-02 06:29:41 -0700
  • 3e75262a3e Reference bias walker Mauricio Carneiro 2013-06-29 11:20:50 -0400
  • 285ab2ac62 Better caching for the HaplotypeCaller Mauricio Carneiro 2013-08-01 20:10:20 -0400
  • 0b062e7f22 Merge pull request #354 from broadinstitute/eb_fix_rr_count_encoding Eric Banks 2013-08-01 12:34:19 -0700
  • e5be038f1a Added error handling to the newly added sites iterator so that it doesn't NPE when it encounters a bad record. Added a unit test that exactly replicates the behavior. Eric Banks 2013-08-01 15:25:20 -0400
  • 1e396af4d0 Two reduce reads updates/fixes: Eric Banks 2013-07-31 10:05:47 -0400
  • ec3c885a25 Merge pull request #353 from broadinstitute/rp_HC_updates_for_1000G_and_WGS_calling Eric Banks 2013-07-31 08:29:06 -0700
  • 4f3411f3d4 Max number of haplotypes to evaluate no longer grows unbounded with the number of samples. This is necessary for multi-sample calling projects with over 100 samples. Ryan Poplin 2013-07-31 10:48:55 -0400
  • 00cedd0bd3 Merge pull request #352 from broadinstitute/yf_SNPEFF_Stratifier Yossi Farjoun 2013-07-30 14:52:33 -0700
  • 284176cd7b moved SnpEffUtilUnitTest to public tree Yossi Farjoun 2013-07-30 17:50:59 -0400
  • b8709b1942 Merge pull request #332 from broadinstitute/st_fpga_hmm droazen 2013-07-30 14:21:21 -0700
  • ac06829194 Merge pull request #349 from broadinstitute/yf_SNPEFF_Stratifier Eric Banks 2013-07-30 12:42:25 -0700
  • d2860a5486 Adding a representation of the hierarchy of flags output by snpEff (Yossi) and a stratifier whose output states are coding regions, genes, stop_gain, stop_lost and splice sites, all determined by the snpEff hierarchy (J. Rose) Joseph Rose 2013-06-06 13:33:20 -0400
  • 7b731dd596 Removed native method call Mauricio Carneiro 2013-07-30 13:59:58 -0400
  • cf46256356 Merge pull request #350 from broadinstitute/chartl_genotypeconcordance_doc_cleanup chartl 2013-07-29 16:17:26 -0700
  • 464a5b229d Add <pre> tags to the Genotype Concordance docs. Tables were not being displayed properly. Chris Hartl 2013-07-29 15:48:17 -0700
  • 678d038c76 Merge pull request #348 from broadinstitute/gg_gatkdoc_fixes Eric Banks 2013-07-26 13:17:51 -0700
  • 3063d82797 Fixed example in CallableLoci gatkdoc Geraldine Van der Auwera 2013-07-25 17:30:42 -0400
  • fc4a8b1dd0 Fixed example in DoC gatkdoc Geraldine Van der Auwera 2013-07-25 17:29:09 -0400
  • 660b075900 Added deprecation notice for SomaticIndelDetector Geraldine Van der Auwera 2013-07-25 17:28:06 -0400
  • 5ad99c362d Added caveat to gatkdocs for MAPQ read transformers & cleaned up AB annotation gatkdocs Geraldine Van der Auwera 2013-07-25 17:20:02 -0400
  • 0ea3f8ca58 Added function to gatkdocs to specify what VCF field an annotation goes in (INFO or FORMAT) Geraldine Van der Auwera 2013-07-25 13:58:54 -0400
  • edbd17b8e0 Added note of caution to VQSR gatkdocs for option BOTH of recalibration mode Geraldine Van der Auwera 2013-07-23 13:27:47 -0400
  • f52196496d Merge pull request #347 from broadinstitute/eb_more_dnagling_tail_improvements Ryan Poplin 2013-07-26 07:25:47 -0700
  • 66db412ad0 Merge pull request #345 from broadinstitute/rp_vqsr_sort_annotations Ryan Poplin 2013-07-26 07:23:42 -0700
  • 8c205dda1b Automatically order the annotation dimensions in the VQSR by their standard deviation instead of the order they were specified on the command line. Ryan Poplin 2013-07-25 12:47:52 -0400
  • 924d9b7ef4 Merge pull request #344 from lbergelson/lb_library_read_filter Eric Banks 2013-07-26 06:44:53 -0700
  • 7c43b5f26a Adding LibraryReadFilter. Louis Bergelson 2013-07-25 13:22:49 -0400
  • 9372c5ef41 Merge pull request #334 from broadinstitute/mc_generic_input_for_qualify_missing_intervals Eric Banks 2013-07-25 12:39:26 -0700
  • 71eb944e62 Adding CnyPairHMMUnitTest sathibault 2013-07-25 14:19:50 -0500
  • 1b25cf471c Merge pull request #341 from broadinstitute/eb_make_all_rr_stranded Eric Banks 2013-07-25 11:50:43 -0700
  • 5dfa863caa Fully stranded implementation of RR (plus bug fix for insertions and het compression). Eric Banks 2013-07-21 23:35:44 -0400
  • 0a2b5ddadf More specific fix for the dangling tail edge case with a single leading deletion. Eric Banks 2013-07-25 11:02:46 -0400
  • 31ab0824b1 quick indentation fixes to FPGA code Mauricio Carneiro 2013-07-24 14:09:49 -0400
  • e5aab22680 Merge pull request #342 from broadinstitute/eb_fix_mq_in_rbp Ryan Poplin 2013-07-24 09:42:13 -0700
  • 6df43f730a Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes. Having them as bytes caused problems for downstream programmers who had data with high MQs. Eric Banks 2013-07-23 23:47:15 -0400
  • 71222bff45 Merge pull request #340 from broadinstitute/eb_fix_okaytomiss_arg Eric Banks 2013-07-21 19:01:01 -0700
  • 672fbe437e Various updates for KB, mostly so that reviews through IGV work properly. Eric Banks 2013-07-19 01:08:40 -0400
  • 224fec7379 parallel test runner: automount triggers David Roazen 2013-07-19 14:13:52 -0400
  • c72880f1d0 build.xml: make ant -p output only important build targets David Roazen 2013-07-19 14:35:00 -0400
  • c7c65502b4 Merge pull request #339 from broadinstitute/gda_1000g_calling Eric Banks 2013-07-19 09:47:39 -0700
  • b0e7ffb931 Committing staging/calling 1000g script to posterity Guillermo del Angel 2013-07-10 13:48:07 -0400
  • b9e3f56c5d Merge pull request #338 from broadinstitute/eb_allow_ceu_trio_in_assessments_again Eric Banks 2013-07-18 21:42:28 -0700
  • b992dcd9c2 Merge pull request #337 from broadinstitute/dr_runtime_sample_renaming_GSA-974 droazen 2013-07-18 12:51:02 -0700
  • 605a5ac2e3 GATK engine: add ability to do on-the-fly BAM file sample renaming at runtime David Roazen 2013-07-03 12:41:01 -0400
  • ca09000584 Allow the CEU trio best practices in the assessments again (it is assigned a low confidence) Eric Banks 2013-07-18 15:18:00 -0400
  • 9121c70510 Fixing merge conflicts. Merged bug fix from Stable into Unstable Eric Banks 2013-07-18 14:43:03 -0400
  • ba531bd5e6 Fixing the 'header is negative' problem in Reduce Reads... again. Eric Banks 2013-06-24 14:06:21 -0400