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  • e40a07bb58 Improve the PairHMM API for better FPGA integration bradtaylor 2013-10-21 14:08:03 -0400
  • f22ab033f6 Merge pull request #424 from broadinstitute/gg_yetanothergatkdocfix Geraldine Van der Auwera 2013-11-13 11:35:59 -0800
  • dac3dbc997 Improved gatkdocs for InbreedingCoefficient, ReduceReads, ErrorRatePerCycle Geraldine Van der Auwera 2013-10-11 10:23:38 -0400
  • 34c8ad529f Merge pull request #423 from broadinstitute/jt_pdexheimer_patch jmthibault79 2013-11-13 04:38:00 -0800
  • 296bcc7fb1 Changed name of jobs submitted to cluster job runners Phillip Dexheimer 2013-11-12 11:42:09 -0500
  • adb939521a Merge pull request #420 from broadinstitute/rp_add_exome_chips_to_knowledge_base Eric Banks 2013-11-08 08:19:17 -0800
  • cd5beca794 Merge pull request #419 from broadinstitute/mc_dpp_updates_part2 MauricioCarneiro 2013-11-07 13:42:32 -0800
  • 725656ae7e Generalizing the FullProcessingPipeline Qscript Mauricio Carneiro 2013-08-22 22:18:47 -0400
  • 1769bcacbc Adding QC'ed versions of the Affy Exome Plus and Broad Exome LOF genotyping results to the knowledgebase. These files include both SNPs and indels. Ryan Poplin 2013-11-07 16:21:23 -0500
  • f15355856a Merge pull request #418 from broadinstitute/eb_fix_liftover_script Eric Banks 2013-11-07 06:04:56 -0800
  • 2fc40a0aed Fixing the liftover script to not require strict VCF header validation. Eric Banks 2013-11-07 09:02:17 -0500
  • f67c3a1b4e Merge pull request #415 from broadinstitute/eb_new_path_for_NIST_in_kb_upload amilev 2013-11-06 13:00:45 -0800
  • 23c9c24adc Various updates to the knowledge base Eric Banks 2013-11-04 10:37:08 -0500
  • 0e3d83d1ef Merge pull request #413 from broadinstitute/rp_qd_and_qual_updates_in_ref_model_pipeline Eric Banks 2013-11-05 06:33:17 -0800
  • 09dfaf1a68 Merge pull request #416 from broadinstitute/mc_quick_fixes_to_cser_pipeline Eric Banks 2013-11-05 06:08:13 -0800
  • a372c0f074 Merge pull request #414 from broadinstitute/eb_update_dbsnp_in_bundle Eric Banks 2013-11-04 07:04:23 -0800
  • 96024403bf Update the dbsnp version in the bundle from 137 to 138; resolves PT #59771004. Eric Banks 2013-11-04 10:01:22 -0500
  • b22c9c2cb4 Improvements to the reference model pipeline. Ryan Poplin 2013-09-30 10:17:43 -0400
  • cafcb34855 Merge pull request #411 from broadinstitute/eb_add_exome_intervals_to_bundle_script Eric Banks 2013-10-29 07:38:44 -0700
  • 209f2a61aa Updated the GATK bundle script to: Eric Banks 2013-10-29 10:33:51 -0400
  • 0ad23c09d5 Merge pull request #410 from lbergelson/lb_missing_script_error kshakir 2013-10-25 08:57:06 -0700
  • 5ed47988b8 Changed the parameter names from cds to baits Mauricio Carneiro 2013-10-24 17:13:25 -0400
  • 9498950b1c Adding more specific error message when one of the scripts doesn't exist. --Previously it gave a cryptic message: ----IO error while decoding blarg.script with UTF-8 ----Please try specifying another one using the -encoding option Louis Bergelson 2013-10-03 16:52:48 -0400
  • 5a2ef37ead Tweak dcov documentation to help prevent user confusion David Roazen 2013-10-16 15:24:33 -0400
  • 1b10d5467a Merge pull request #409 from broadinstitute/rp_postQC_titv_ratio_smoothing Ryan Poplin 2013-10-16 07:41:37 -0700
  • e9d0d6ada0 Smooth over ti/tv bins with small numbers of counts in the PostCallingQC script Ryan Poplin 2013-10-16 10:40:50 -0400
  • 93d525b56c Merge pull request #407 from broadinstitute/mc_dwn_exome MauricioCarneiro 2013-10-10 11:56:12 -0700
  • b248a61db6 Merge pull request #408 from broadinstitute/gda_more_pool_caller_stuff MauricioCarneiro 2013-10-10 11:55:17 -0700
  • 36e92a3323 More script committing for posterity - Pool Caller scripts with last minute fixes. Also committed script that plotted 1000G FDR that I used in ASHG2012. Added also a README.txt file in /humgen/gsa-hpprojects/dev/validationExperiments/largeScaleValidation/finalPaperData/README.txt in case things need to get run again. Guillermo del Angel 2013-07-19 13:41:20 -0400
  • efbfdb64fe Qscript to Downsample and analyze an exome BAM Mauricio Carneiro 2013-08-19 23:52:23 -0400
  • 9d932e8c60 Merged bug fix from Stable into Unstable Chris Hartl 2013-10-10 14:31:33 -0400
  • 6f46d1187a Remember to copy the integration test changes *as well as* the walker changes Chris Hartl 2013-10-10 14:30:37 -0400
  • 55bab9fa87 Merged bug fix from Stable into Unstable Chris Hartl 2013-10-10 13:01:12 -0400
  • 06d28c7f8b VariantsToBinaryPed: Move .fam file writing to initialize to ensure ordering matches the ordering of the VCF. Change the documentation to clarify that the fam files are not directly copied, but subset and re-ordered. Chris Hartl 2013-10-10 12:53:15 -0400
  • 5d6421494b Fix mismatching number of columns in report Mauricio Carneiro 2013-10-09 14:38:15 -0400
  • e9a93d23c3 Merge pull request #405 from broadinstitute/eb_fix_ugcallvariants Eric Banks 2013-10-08 08:36:06 -0700
  • b71691f5a3 Don't keep the original QUAL. The whole point of this private walker is to regenerate it! Eric Banks 2013-10-08 11:34:14 -0400
  • 8ebb288014 Auto-restart Bamboo on gsa4 in the event of a crash David Roazen 2013-10-07 16:10:17 -0400
  • 385c8d4a70 Place a copy of gsa-engineering's gsa4 crontab under version control David Roazen 2013-10-07 14:44:56 -0400
  • d6fcebf948 Make cron daemon-spawning scripts less chatty David Roazen 2013-10-07 14:35:59 -0400
  • 49d489cbf8 Merge pull request #393 from broadinstitute/mc_qualify_updates_for_cser Eric Banks 2013-10-04 09:50:39 -0700
  • 63ace685c9 add unit tests Mauricio Carneiro 2013-09-10 10:59:27 -0400
  • 839b918f58 Length metric updates to QualifyMissingIntervals Mauricio Carneiro 2013-09-09 16:10:39 -0400
  • 3aef87c214 Merge pull request #403 from broadinstitute/gg_vqsr_disable_plot Ryan Poplin 2013-09-30 17:06:51 -0700
  • 9f7fa247f6 Disable VQSR tranche plots in INDEL mode Geraldine Van der Auwera 2013-09-26 16:04:08 -0400
  • 749903325e Merge pull request #404 from broadinstitute/rp_reference_model_bug_fix_blocksize_annotation Eric Banks 2013-09-30 06:06:01 -0700
  • ef1d58b7ff Bugfix for hom ref records that aren't GVCF blocks. Ryan Poplin 2013-09-27 11:24:35 -0400
  • f3a67edc24 Merge pull request #402 from broadinstitute/gg_dcov_docs Ryan Poplin 2013-09-27 07:07:21 -0700
  • cba9668641 Merge pull request #401 from broadinstitute/gg_vqsr_ignorefilter_doc Ryan Poplin 2013-09-27 07:05:41 -0700
  • a29f1f84bf Merge pull request #397 from lbergelson/lb_scala_2.10.2 kshakir 2013-09-26 21:51:43 -0700
  • 511948890a Modify gatkdoc template to handle downsampling info better Geraldine Van der Auwera 2013-09-26 14:50:32 -0400
  • 66d0235efc Minor clarifications & formatting tweaks for dcov docs Geraldine Van der Auwera 2013-09-26 14:28:22 -0400
  • 27808d336a Minor clarifications regarding ignoreFilter argument Geraldine Van der Auwera 2013-09-26 13:13:53 -0400
  • a9fa5206ee Merge pull request #399 from broadinstitute/eb_update_docs_for_DepthPerSampleHC Geraldine Van der Auwera 2013-09-25 15:20:19 -0700
  • f362597f69 Merge pull request #400 from broadinstitute/mm_bugfix_combine_variants_implicit_casting Ryan Poplin 2013-09-25 11:47:17 -0700
  • 5113e21437 Bug fix: annotation values ar parsed as Doubles when they should be parsed as Integers due to implicit conversion. * Updated expected test data in which an integer annotation (MQ0) was formatted as a double. Michael McCowan 2013-09-23 14:26:24 -0400
  • 41fef329b4 Update scripts for depristo -> gsa-engineering migration David Roazen 2013-09-25 12:57:49 -0400
  • 2783c84c6b Updated docs for DepthPerSampleHC to deliver PT #54237024. Eric Banks 2013-09-24 22:32:19 -0400
  • 66b51dbc0f Merge pull request #398 from broadinstitute/eb_update_indel_model_arg_docs Eric Banks 2013-09-23 12:51:18 -0700
  • d6992d1263 Updated docs to tell users not to use PCR indel error modeling for PCR free data. Eric Banks 2013-09-23 15:48:47 -0400
  • c05208ecec Resolving warnings --specifying exception types in cases where none was already specified ----mostly changed to catch Exception instead of Throwable ----EmailMessage has a point where it should only be expecting a RetryException but was catching everything Louis Bergelson 2013-08-30 16:43:21 -0400
  • b32ad99d3f Changing from scala 2.9.2 to 2.10.2. --modified ivy dependencies --modified scala classpath in build.xml to include scala-reflect Louis Bergelson 2013-08-27 15:56:30 -0400
  • 5bbad75402 Changing max coverage threshold Mauricio Carneiro 2013-09-20 18:54:01 -0400
  • 175388de1d Merge pull request #396 from broadinstitute/mc_dt_excessive_coverage_defaults Geraldine Van der Auwera 2013-09-20 15:12:16 -0700
  • 5e2ffc74fc Automated interpretation for QualifyMissingIntervals Mauricio Carneiro 2013-09-20 16:47:12 -0400
  • 74639463b9 Updating excessive coverage default parameter Mauricio Carneiro 2013-09-19 23:07:20 -0400
  • 713c988404 Merge pull request #395 from broadinstitute/dr_chapmanb_patch_add_api_close_methods droazen 2013-09-11 10:25:54 -0700
  • 2f5064dd1d Provide close methods to clean up resources used while creating AlignmentContexts from BAM file regions. Allows utilization of CoveredLocusView via the API chapmanb 2013-08-12 14:36:57 -0400
  • 5e539bb11b Merge pull request #394 from broadinstitute/rp_single_sample_calling_pipeline_update Ryan Poplin 2013-09-10 07:12:05 -0700
  • 292426b504 Merge pull request #390 from broadinstitute/mc_update_clipreads Geraldine Van der Auwera 2013-09-09 16:43:03 -0700
  • 8b829255e7 Clarified docs on using clipping options Geraldine Van der Auwera 2013-09-09 19:40:03 -0400
  • 8971861fd0 Updates to the single sample calling pipeline to reflect latest experiments with full whole genome callsets. Ryan Poplin 2013-09-09 15:32:21 -0400
  • 014bc4269e Merge pull request #361 from broadinstitute/bt_pairhmm_array_implementation MauricioCarneiro 2013-09-08 20:16:53 -0700
  • 08474a39fb Merge pull request #389 from broadinstitute/rp_single_sample_calling_pipline_HC Ryan Poplin 2013-09-06 14:35:51 -0700
  • 3503050a39 Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller Ryan Poplin 2013-08-08 15:09:38 -0400
  • b6c3ed0295 Added REVERT SOFTCLIPPED bases to ClipReads Mauricio Carneiro 2013-09-06 09:30:01 -0400
  • add17dc463 Merge pull request #388 from broadinstitute/eb_change_record_size_mismatch_to_user_error Ryan Poplin 2013-08-30 10:29:54 -0700
  • ea0deb1bb2 Changed the error for the record size mismatch in the genotyping engine to be a user error since it is possible to reach this state with input VCFs that contain the same event multiple times (and it's not something we want to handle in the code). Eric Banks 2013-08-30 12:18:19 -0400
  • 5d79a6cbe0 Merge pull request #387 from lbergelson/lb_add_ungenotyped_case_countvariants Eric Banks 2013-08-30 06:14:08 -0700
  • 4473b0065e adding a check for the UNAVAILABLE case of GenotypeType in CountVariants Louis Bergelson 2013-08-29 11:23:47 -0400
  • 0435bbe38f Retreived PairHMM benchmarks from archive and made improvements bradtaylor 2013-08-18 21:24:58 -0400
  • 86fe9fae76 Changes to Array PairHMM to address review comments bradtaylor 2013-08-07 18:27:30 -0400
  • 3671e41b0c Add Array Logless PairHMM bradtaylor 2013-06-11 17:04:19 -0400
  • 7479152977 Merged bug fix from Stable into Unstable Ryan Poplin 2013-08-28 12:40:25 -0400
  • 6bda569666 One of the log10sumLog10s in the VQSR was missed in a previous bug fix. Thanks to Mike McCowan for spotting this one. Ryan Poplin 2013-08-28 12:40:08 -0400
  • 983097cff2 Merge pull request #385 from broadinstitute/gg_vqsr_docfixes Eric Banks 2013-08-26 17:42:47 -0700
  • ed465cd2a5 Fixed a few typos and clarified some doc points. Geraldine Van der Auwera 2013-08-26 17:33:17 -0400
  • 42d771f748 Remove org.apache.commons.collections.IteratorUtils dependency from the test suite David Roazen 2013-08-21 19:41:34 -0400
  • 4b00c81181 Merge remote-tracking branch 'unstable/master' Eric Banks 2013-08-21 17:12:26 -0400
  • 38b80a5916 Merge pull request #384 from broadinstitute/eb_pbt_dropping_multiallelics Eric Banks 2013-08-21 14:09:32 -0700
  • 9424008055 Merge pull request #383 from broadinstitute/dr_change_phone_home_aws_settings Eric Banks 2013-08-21 14:08:21 -0700
  • d4dc5ba04a Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records. Eric Banks 2013-08-21 15:46:57 -0400
  • 9fbb4920d0 Update GATK AWS phone-home configuration David Roazen 2013-08-21 12:39:30 -0400
  • cdfd07f9eb Merge pull request #382 from broadinstitute/ami-FixBcfCoder-52571227 Eric Banks 2013-08-21 11:29:19 -0700
  • 0f5bb706ff - update picard, sam, variants and tribble after fixing bug in BCF2Utils.makeDictionary as reported in ticket 52571227 - update call for VCFSimpleHeaderLine constructor in GATKVCFUtils Ami Levy-Moonshine 2013-08-21 12:06:42 -0400
  • ec0c33890a change the dbsnp version from 137 to 129 for variantEval Ami Levy-Moonshine 2013-07-11 14:45:21 -0400
  • e1174a582d Merge pull request #379 from broadinstitute/mc_dpp_updates_part2 Eric Banks 2013-08-19 18:42:12 -0700
  • 6663d48ffe Merge pull request #381 from broadinstitute/mm_rev_picard_to_get_tribble_updates Eric Banks 2013-08-19 18:31:02 -0700
  • c3a933ce84 Adaptations to accomodate Tribble API changes, comprising mostly of the following. * Refactoring implementations of readHeader(LineReader) -> readActualHeader(LineIterator), including nullary implementations where applicable. * Galvanizing fo generic types. * Test fixups, mostly to pass around LineIterators instead of LineReaders. * New rev of tribble, which incorporates a fix that addresses a problem with TribbleIndexedFeatureReader reading a header twice in some instances. * New rev of sam, to make AbstractIterator visible (was moved from picard -> sam in Tribble API refactor). Michael McCowan 2013-08-19 12:42:28 -0400
  • e991307eb5 Including SplitByRG in the FullProcessingPipeline Mauricio Carneiro 2013-08-15 11:54:49 -0400