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  • f5a301fb63 Bugfix for AlignmentUtils.trimCigarByBases Mark DePristo 2013-04-23 18:26:20 -0400
  • 2bcbdd469f leftAlignCigarSequentially now supports haplotypes with insertions and deletions where the deletion allele was previously removed by the leftAlignSingleIndel during it's cleanup phase. Mark DePristo 2013-04-19 16:11:29 -0400
  • aefddaa219 Merge pull request #210 from broadinstitute/gda_QUAL_fix_GSA-910 Eric Banks 2013-05-03 06:28:10 -0700
  • 4f627e96c0 Merge pull request #211 from broadinstitute/md_kb_script Mark DePristo 2013-05-03 04:30:23 -0700
  • b89d97cb9c Starting NA12878 KB requires use Java-1.7 Mark DePristo 2013-05-03 07:29:29 -0400
  • 0c30a5ebc6 Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VALUE) when converting from GL to integers. Increase capping to Integer.MAX_VALUE (2^31-1) which should be enough for reasonable sites now. Integration tests change because some tests have some hyper-deep pileups where this case was hit Guillermo del Angel 2013-05-01 15:25:23 -0400
  • c6df20cff5 Merge pull request #209 from broadinstitute/eb_more_fixes_to_bundle_script Eric Banks 2013-05-02 12:23:41 -0700
  • d981fd01b8 Now that we don't generate dict and fai files, the resource script needs to copy them to the bundle. Eric Banks 2013-05-02 15:18:13 -0400
  • 13bfa963da Revert changes to exampleFASTA.fasta.fai for now to get tests passing again David Roazen 2013-05-02 12:59:20 -0400
  • dfdc0df4f1 Merge pull request #207 from broadinstitute/eb_fixing_bundle_script Mark DePristo 2013-05-02 08:18:19 -0700
  • f88a964e2c Adding .fai file to example fasta since we don't generate it anymore Eric Banks 2013-05-02 10:54:32 -0400
  • 6d0e383a60 Fixing the bundle script Eric Banks 2013-05-02 09:28:40 -0400
  • 4b8b411b92 - Fixed a small bug in the printout of molten data in GenotypeConcordance Output didn't "mix-up" the genotypes, it outputed the same HET vs HET (e.g.) 3 times rather than the combinations of HET vs {HET, HOM, HOM_REF}, etc. This was only a problem in the text, _not_ the actual numbers, which were outputted correctly. Yossi Farjoun 2013-05-01 12:45:03 -0400
  • 803f666fd5 Merge pull request #204 from broadinstitute/rp_cgl_force_sample_name Mark DePristo 2013-05-01 13:59:20 -0700
  • ad84f15572 Adding argument to CGL to not stratify by sample name. This is useful when running with 1000G so that you don't get 1000s of lines on the plots. Ryan Poplin 2013-05-01 12:22:27 -0400
  • 19b59f0fb9 Merge pull request #206 from broadinstitute/dr_update_tests_for_java7 droazen 2013-05-01 13:23:25 -0700
  • f3c94a3c87 Update expected test output for Java 7 David Roazen 2013-05-01 15:48:05 -0400
  • d0980e236a Merged bug fix from Stable into Unstable David Roazen 2013-05-01 01:08:29 -0400
  • f57256b6c2 Delete unused FastaSequenceIndexBuilder class and accompanying test David Roazen 2013-05-01 01:02:01 -0400
  • 2edb286d1c Merged bug fix from Stable into Unstable David Roazen 2013-04-30 22:33:36 -0400
  • 3390fc7d67 Include cofoja jar in classpath when testing release jars David Roazen 2013-04-30 22:16:58 -0400
  • e29b52b9a5 Merge remote-tracking branch 'unstable/master' Eric Banks 2013-04-30 15:31:33 -0400
  • a0a1a366e3 Merge pull request #201 from broadinstitute/eb_fix_reduced_count_tagging Mark DePristo 2013-04-30 12:14:40 -0700
  • 58424e56be Setting the reduce reads count tag was all wrong in a previous commit; fixing. Eric Banks 2013-04-29 11:17:38 -0400
  • 15266da51c Merge pull request #203 from broadinstitute/gda_poolcaller_paper delangel 2013-04-30 07:12:02 -0700
  • 95637e03a0 Updates to pool caller scala script due to new paths and cleanup, hopefully with final changes for paper. Added also R script used to process everything into a couple of ggplot-friendly data frames. Functionality is basically the same. Enhancements: -- Add annotation to log axiom and Exome Chip AC along with LOF results for concordance comparisons. -- General Cleanup. -- Used base path for files as a variable in case directory structure in gsa-hpprojects changes again. -- Output also per-pool data by subsetting genotypes per pool and comparing with corresponding genotypes from Axiom, exome chip and omni. -- Commit R scripts that load all tables and crunch them to analyze them. Guillermo del Angel 2013-02-15 12:28:13 -0500
  • 6ea2bceb55 Merge pull request #202 from broadinstitute/yf_remove_getlength_from_every_GATKBAMIndex_read Mark DePristo 2013-04-30 06:24:34 -0700
  • 73fcacbf1b Change Long to long Mark DePristo 2013-04-30 09:21:10 -0400
  • a3a2ec5a1c Merge pull request #200 from broadinstitute/gda_ug_rr_bug_48742591 Eric Banks 2013-04-29 17:54:43 -0700
  • 20d3137928 Fix for indel calling with UG in presence of reduced reads: When a read is long enough so that there's no reference context available, the reads gets clipped so that it falls again within the reference context range. However, the clipping is incorrect, as it makes the read end precisely at the end of the reference context coordinates. This might lead to a case where a read might span beyond the haplotype if one of the candidate haplotypes is shorter than the reference context (As in the case e.g. with deletions). In this case, the HMM will not work properly and the likelihood will be bad, since "insertions" at end of reads when haplotype is done will be penalized and likelihood will be much lower than it should. -- Added check to see if read spans beyond reference window MINUS padding and event length. This guarantees that read will always be contained in haplotype. -- Changed md5's that happen when long reads from old 454 data have their likelihoods changed because of the extra base clipping. Guillermo del Angel 2013-04-28 09:14:35 -0400
  • 0e7e6d35d8 GATKBAMIndex calls buffer.length() on every read. This is causing much pain. Optimized by getting the read of the file upon opening the index-file and using that instead. Yossi Farjoun 2013-04-29 12:49:02 -0400
  • c5701a9ade Merge pull request #199 from broadinstitute/md_clipped_reduced_reads Eric Banks 2013-04-29 09:14:43 -0700
  • 0387ea8df9 Bugfix for ReadClipper with ReducedReads Mark DePristo 2013-04-29 10:05:18 -0400
  • 5dd73ba2d1 Merge pull request #198 from broadinstitute/mc_reduce_reads_ds_doc Mark DePristo 2013-04-27 05:49:47 -0700
  • 651e1f23b1 Merge pull request #194 from broadinstitute/gda_ancient_dna_newPipeline delangel 2013-04-27 04:59:09 -0700
  • 76e997895e Updates GATKDocs for ReduceReads downsampling Mauricio Carneiro 2013-04-26 23:33:09 -0400
  • 4168aaf280 Add feature to specify Allele frequency priors by command line when calling variants. Guillermo del Angel 2013-04-26 15:49:31 -0400
  • 759c531d1b Merge pull request #197 from broadinstitute/dr_disable_snpeff_version_check Mark DePristo 2013-04-26 13:55:14 -0700
  • 7d90bbab08 Add support for snpEff "GATK compatibility mode" (-o gatk) David Roazen 2013-04-26 13:42:01 -0400
  • ec8fb9860a Merge pull request #196 from broadinstitute/rp_cgl_allele_matching Mark DePristo 2013-04-26 12:38:59 -0700
  • 93fc48739a In CGL ensure that the alleles match exactly between the comp track and the external likelihoods track. Ryan Poplin 2013-04-26 14:20:33 -0400
  • 071fd67d55 Merge pull request #193 from broadinstitute/eb_contamination_fixing_for_reduced_reads Mark DePristo 2013-04-26 09:48:45 -0700
  • 92a6c7b561 Merge pull request #195 from broadinstitute/eb_exclude_sample_file_bug_in_select_variants Mark DePristo 2013-04-26 09:47:38 -0700
  • 360e2ba87e Fixed bug reported on the forum where using the --exclude_sample_file argument in SV was giving bad results. Eric Banks 2013-04-26 12:23:11 -0400
  • 021adf4220 WTF - I thought we had disabled the randomized dithering of rank sum tests for integration tests?! Eric Banks 2013-04-25 15:39:42 -0400
  • ba2c3b57ed Extended the allele-biased down-sampling functionality to handle reduced reads. Eric Banks 2013-04-24 11:52:26 -0400
  • b749f06ba6 Merge pull request #192 from broadinstitute/dr_rev_picard_for_2.5_release droazen 2013-04-25 17:59:27 -0700
  • 7cb1247164 Rev picard, sam-jdk, tribble, and variant jars to version 1.90.1442 David Roazen 2013-04-25 13:53:32 -0400
  • 528c3d083a Merge pull request #191 from broadinstitute/dr_fix_rod_system_locking Mark DePristo 2013-04-25 09:32:54 -0700
  • 3c7db87527 Merge pull request #189 from broadinstitute/md_hc_clip_before_merging Ryan Poplin 2013-04-25 08:42:03 -0700
  • d20be41fee Bugfix for FragmentUtils.mergeOverlappingPairedFragments Mark DePristo 2013-04-24 17:22:07 -0400
  • 4d56142163 Detect stuck lock-acquisition calls, and disable file locking for tests David Roazen 2013-04-11 13:04:29 -0400
  • 43f1746eb9 Merge pull request #190 from broadinstitute/mc_processing_pipeline Mark DePristo 2013-04-24 17:04:46 -0700
  • 95ac9b6a33 TechDev version of the Data Processing Pipeline Mauricio Carneiro 2013-04-24 19:51:34 -0400
  • 55ead98d3d Merge pull request #188 from broadinstitute/gda_cgl_fix Mark DePristo 2013-04-24 16:17:29 -0700
  • 3d49f524ee Small fixes for CalibrateGenotypeLikelihoods. -- If we are using an external vcf, do not consider filtered out records when argument -ignoreFiltered is set. -- Fix for R script: it uses ddply but some default R installations don't include plyr library by default. Guillermo del Angel 2013-04-24 18:41:40 -0400
  • 27bb699e8b Merge pull request #181 from broadinstitute/eb_yet_more_rr_improvements_GSA-930 MauricioCarneiro 2013-04-24 15:40:03 -0700
  • 379a9841ce Various bug fixes for recent Reduce Reads additions plus solution implemented for low MQ reads. Eric Banks 2013-04-17 12:45:09 -0400
  • 45fec382e7 Merge pull request #180 from broadinstitute/mc_diagnosetargets_missing_targets MauricioCarneiro 2013-04-24 14:54:55 -0700
  • 3f52f55c55 Merge pull request #186 from broadinstitute/md_libs_canonical_cigar Eric Banks 2013-04-24 12:58:32 -0700
  • 367f0c0ac1 Split class names into stratification and metrics Mauricio Carneiro 2013-04-24 14:15:49 -0400
  • 91d5674cc5 Merge pull request #187 from broadinstitute/rp_new_bundle_for_release Mark DePristo 2013-04-24 08:44:38 -0700
  • 80131ac996 Adding the 1000G_phase1.snps.high_confidence callset to the GATK resource bundle for use in the April 2013 updated best practices. Ryan Poplin 2013-04-24 11:41:32 -0400
  • df90597bfc Performance optimizations and caliper benchmarking code for consolidateCigar Mark DePristo 2013-04-19 17:31:59 -0400
  • df6ba74395 Merge pull request #185 from broadinstitute/gda_poolcaller_fix_47921867 Mark DePristo 2013-04-24 04:14:05 -0700
  • 2ab270cf3f Corner case fix to General Ploidy SNP likelihood model. -- In case there are no informative bases in a pileup but pileup isn't empty (like when all bases have Q < min base quality) the GLs were still computed (but were all zeros) and fed to the exact model. Now, mimic case of diploid Gl computation where GLs are only added if # good bases > 0 -- I believe general case where only non-informative GLs are fed into AF calc model is broken and yields bogus QUAL, will investigate separately. Guillermo del Angel 2013-04-23 17:51:46 -0400
  • 8f8f339e4b Abstract class for the statistics Mauricio Carneiro 2013-04-23 18:02:27 -0400
  • e83d9bef59 Merge pull request #182 from broadinstitute/md_hc_vqsr_best_practices Ryan Poplin 2013-04-23 12:49:10 -0700
  • 90fc249c8d Merge pull request #184 from broadinstitute/rp_revert_sw_params Mark DePristo 2013-04-23 12:32:13 -0700
  • cb2a8f83de Merge pull request #183 from jsilter/master Mark DePristo 2013-04-23 11:59:52 -0700
  • 75184614c6 Add additional necessary class files to na12878kb.jar target Jacob Silterra 2013-04-23 14:03:48 -0400
  • 38662f1d47 Limiting access to the DT classes Mauricio Carneiro 2013-04-23 14:01:43 -0400
  • d5d87c50e6 Updates to GeneralCallingPipeline Mark DePristo 2013-04-04 17:57:20 -0400
  • cb4ec3437a After debate reverting SW parameter changes temporarily while we explore global SW plans. Ryan Poplin 2013-04-23 13:32:06 -0400
  • fdd16dc6f9 DiagnoseTargets refactor Mauricio Carneiro 2013-04-20 21:49:50 -0400
  • eb6308a0e4 General DiagnoseTargets documentation cleanup Mauricio Carneiro 2013-04-20 18:34:03 -0400
  • b3c0abd9e8 Remove REF_N status from DiagnoseTargets Mauricio Carneiro 2013-04-20 14:42:33 -0400
  • 2b923f1568 fix for DiagnoseTargets multiple filter output Mauricio Carneiro 2013-04-20 13:05:14 -0400
  • cf7afc1ad4 Fixed "skipped intervals" bug on DiagnoseTargets Mauricio Carneiro 2013-04-20 00:28:35 -0400
  • ff430c821e Merge pull request #178 from broadinstitute/md_common_suffix_bugfix Ryan Poplin 2013-04-22 06:53:01 -0700
  • be66049a6f Bugfix for CommonSuffixSplitter Mark DePristo 2013-04-21 15:42:26 -0400
  • fc29a66a63 Merge pull request #177 from broadinstitute/md_gatklog_cleanup Mark DePristo 2013-04-20 11:08:06 -0700
  • 7e88a12bf1 Delete progress log when script is done for downloadGATKReportsFromS3.csh Mark DePristo 2013-04-20 14:06:02 -0400
  • 12ac60ac3a Merge pull request #175 from broadinstitute/eb_increase_log10_cache_size Eric Banks 2013-04-19 05:43:07 -0700
  • 3477e092ea Minor: bump up the amount of cached log10 data in MathUtils so that Monkol can actually call 50K samples. Eric Banks 2013-04-19 08:39:08 -0400
  • ef8679c0a0 Merge pull request #174 from broadinstitute/md_hc_parameters Ryan Poplin 2013-04-17 12:33:42 -0700
  • f0e64850da Two sensitivity / specificity improvements to the haplotype caller Mark DePristo 2013-04-17 10:30:37 -0400
  • b27706859a Merge pull request #172 from broadinstitute/eb_reducereads_het_improvements MauricioCarneiro 2013-04-16 16:48:10 -0700
  • 5bce0e086e Refactored binomial probability code in MathUtils. Eric Banks 2013-04-09 15:37:08 -0400
  • df189293ce Improve compression in Reduce Reads by incorporating probabilistic model and global het compression Eric Banks 2013-04-08 14:01:57 -0400
  • 8e6309d56e Merge pull request #171 from broadinstitute/rp_hc_restore_filter_function Mark DePristo 2013-04-16 11:21:32 -0700
  • e0dfe5ca14 Restore the read filter function in the HaplotypeCaller. Ryan Poplin 2013-04-16 09:37:04 -0400
  • e176fc3af1 Merge pull request #159 from broadinstitute/md_bqsr_ion Geraldine Van der Auwera 2013-04-16 08:54:47 -0700
  • 936f4da1f6 Merge pull request #166 from broadinstitute/md_hc_persample_haplotypes Ryan Poplin 2013-04-16 08:46:56 -0700
  • bfbc23e99e Merge pull request #173 from broadinstitute/md_fix_vqsr Mark DePristo 2013-04-16 08:46:26 -0700
  • 17982bcbf8 Update MD5s for VQSR header change Mark DePristo 2013-04-16 11:45:45 -0400
  • 067d24957b Select the haplotypes we move forward for genotyping per sample, not pooled Mark DePristo 2013-04-16 09:30:06 -0400
  • 0ee21e58c3 Merge pull request #165 from broadinstitute/md_vqsr_improvements Ryan Poplin 2013-04-16 06:26:38 -0700
  • 5a74a3190c Improvements to the VariantRecalibrator R plots Mark DePristo 2013-04-11 10:52:59 -0400
  • 564fe36d22 VariantRecalibrator's VQSR.vcf now contains NEG/POS labels Mark DePristo 2013-04-05 09:28:46 -0400