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  • d3c84e7b1f This should be a User Error since it's provided from the DoC command-line arguments Eric Banks 2012-04-18 13:09:23 -0400
  • 392f1903f7 Handling some of the NumberFormatExceptions seen via Tableau that are really user errors. Eric Banks 2012-04-18 12:57:37 -0400
  • 70777c7af8 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-04-18 12:42:28 -0400
  • 5d3c764ed2 Cleaned up the DoC code and made the pseq commands a little more robust to non-standard chromosomes Menachem Fromer 2012-04-18 12:41:32 -0400
  • 8a84456626 Following Eric's awesome update to change the VQSR recal file into a VCF file, the ApplyRecalibration step is now scatter/gather-able and tree reducible. Ryan Poplin 2012-04-18 11:24:04 -0400
  • 333ae3bc2c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-04-17 23:54:16 -0400
  • 4448a3ea76 Final tweaks. Added an integration test to cover the case of SNPs and indels that start at the same position. Eric Banks 2012-04-17 23:54:10 -0400
  • 2fba7df0a6 Updating integration tests for new BQSR output Mauricio Carneiro 2012-04-17 23:39:40 -0400
  • c1f52b773a Minor tweaks and updated integration tests MD5s Eric Banks 2012-04-17 23:17:28 -0400
  • 6d03bce0d3 Important refactoring of the VQSR recal file format: we now use a VCF instead of a CSV file. Eric Banks 2012-04-17 22:38:18 -0400
  • ea793d8e27 Khalid pressured me into adding an integration test that makes sure we don't fail on reads with adjacent I and D events. Eric Banks 2012-04-17 21:21:29 -0400
  • 00bef8f33b Must provide output as argument so that command-line string is constructed properly Menachem Fromer 2012-04-17 20:50:11 -0400
  • e3bc1e8630 Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Menachem Fromer 2012-04-17 20:33:45 -0400
  • 4ff9cbd7e9 Added more support for XHMM options (and can now use Plink/Seq to calculate repeat-masked intervals since GATK and reference do not have this encoded in lower-case bases) Menachem Fromer 2012-04-17 20:33:02 -0400
  • 46a212d8e9 Added "simplify reads" option to PrintReads. Mauricio Carneiro 2012-04-12 14:09:18 -0400
  • f0c81b59b0 Implementation of the new BQSR plotting infrastructure Mauricio Carneiro 2012-04-12 13:52:32 -0400
  • 952280bef1 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-04-17 17:00:14 -0400
  • cf705f6c62 Adding read position rank sum test to the list of annotations that get produced with the HaplotypeCaller Ryan Poplin 2012-04-17 17:00:00 -0400
  • 4ced094160 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-04-17 15:51:37 -0400
  • 13c800417e Handle NPE in UG indel code: deletions immediately preceding insertions were not handled well in the code. Eric Banks 2012-04-17 15:51:23 -0400
  • c78b0eee3a Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. Guillermo del Angel 2012-04-17 14:22:48 -0400
  • 08a1ef2681 Fixing the issue identified by Guillermo where the last base of read wasn't being considered in the non-global alignment PairHMM. Added his unit tests to catch this case. Ryan Poplin 2012-04-17 14:01:43 -0400
  • 91cb654791 AggregateMetrics: - By porting from jython to java now accessible to Queue via automatic extension generation. - Better handling for problematic sample names by using PicardAggregationUtils. GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name. CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering. Added SelectHeaders walker for filtering headers for dbGAP submission. Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter. Latest WholeGenomePipeline. Other minor cleanup to utility methods. Khalid Shakir 2012-04-17 11:45:32 -0400
  • 1a2e92f8db Merged bug fix from Stable into Unstable Ryan Poplin 2012-04-17 10:23:05 -0400
  • adad76b36f Fixing NPE in VQSR for the case of very small callsets. Ryan Poplin 2012-04-17 10:20:43 -0400
  • 282b4afdca Licenses for GATK 1 and 2 beta Mark DePristo 2012-04-17 11:40:02 +0100
  • 87be63c7e4 Improve variantCallQC.R Mark DePristo 2012-04-13 16:59:15 -0400
  • 3f6b2423d8 Update VE IT to reflect new fields and bugfixes Mark DePristo 2012-04-13 11:56:48 -0400
  • f9190b6fcd VariantEvalUnitTest is better named VariantEvalWalkerUnitTest Mark DePristo 2012-04-13 11:24:33 -0400
  • 23ccf772d4 IndelSummary now emits all of the underlying counts for ratios, percentages, etc it computes Mark DePristo 2012-04-13 11:21:02 -0400
  • 542a8e3306 No longer stratify ratio_of_1_and_2_to_3_bp_insertions by 1bp context Mark DePristo 2012-04-11 09:44:01 -0400
  • 84d1e8713a Infrastructure for combining VariantEvaluations Mark DePristo 2012-04-11 09:41:45 -0400
  • 38986e4240 Documentation for StratificationManager Mark DePristo 2012-04-10 13:54:20 -0400
  • ab06d53867 Useful test constructor or Unit tests in RefMetaDataTracker Mark DePristo 2012-04-10 09:34:28 -0400
  • 285e61a227 Bugfix for IndelSummary Mark DePristo 2012-04-10 08:31:09 -0400
  • adc519f7d1 VariantCallQC improvements Mark DePristo 2012-04-09 16:49:42 -0400
  • e6d5cb46d2 Improvements and bugfixes to IndelSummary Mark DePristo 2012-04-09 15:51:34 -0400
  • bfa966a4e9 Bugfix for OneBPIndel Mark DePristo 2012-04-09 15:50:20 -0400
  • 2aa2d9aec0 Merged bug fix from Stable into Unstable Mark DePristo 2012-04-13 09:25:43 -0400
  • 27e7e17dc7 New way to handle exceptions in multi-threaded GATK Mark DePristo 2012-04-13 09:23:20 -0400
  • e85e9a8cf5 More extensive testing of type of error thrown in multi-threaded walker test Mark DePristo 2012-04-12 14:42:40 -0400
  • 297afc7911 Added unit test to ensure that we genotype correctly cases with really large GLs Eric Banks 2012-04-12 15:43:14 -0400
  • 818e8c2fb9 Resolving merge conflicts Eric Banks 2012-04-12 15:19:44 -0400
  • 0dd571928d Let's not have the indel model emit more than the max possible number of genotypable alt alleles (since we may not be able to subset down to the best ones). Eric Banks 2012-04-12 15:16:29 -0400
  • 4004ec3e6f Preemptive bug fixes in CalibrateGenotypeLikelihoods: prevent null pointer exception if we're in indels mode and truth file happens to have a snp or mixed record Guillermo del Angel 2012-04-12 14:10:09 -0400
  • f77a6d18b8 Bad conflict merge before Eric Banks 2012-04-12 09:56:49 -0400
  • 33a8bdd75f Resolving merge conflicts Eric Banks 2012-04-12 09:51:55 -0400
  • b659b16b31 Generate User Error for bad POS value Eric Banks 2012-04-12 09:49:35 -0400
  • cc71baf691 Don't allow users to try to genotype more than the max possible value (catch and throw a User Error at startup). Better docs explaining that users shouldn't play with this value unless they know what they are doing. Eric Banks 2012-04-12 09:18:44 -0400
  • 5bf9dd2def A framework to get annotations working in the HaplotypeCaller (and ART walkers in general). Eric Banks 2012-04-11 14:43:40 -0400
  • f9f8589692 Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. Guillermo del Angel 2012-04-11 13:56:51 -0400
  • 5b7da3831f Not sure why this didn't make it into the last push, but here's a working MD5 for the NDA annotation in UG Eric Banks 2012-04-11 13:49:50 -0400
  • 7aa654d13f New interface for some dev work that Ryan and I are doing; only accessible from private walkers right now Eric Banks 2012-04-11 13:49:09 -0400
  • dc90508104 Adding a new annotation to UG calls: NDA = number of discovered (but not necessarily genotyped) alleles for the site. This could help downstream analysis esp. of indels for wonky sites (since we only use the top 2-3 alleles). Not enabled by default but we can change that if this turns out to be useful. Eric Banks 2012-04-11 13:47:10 -0400
  • d2142c3aa7 Adding integration test for Flag Stat Eric Banks 2012-04-10 22:40:38 -0400
  • f560611fe8 Merged bug fix from Stable into Unstable Eric Banks 2012-04-10 22:26:53 -0400
  • f46f7d0590 Fix the stats coming out of FlagStat. I will add an integration test in unstable Eric Banks 2012-04-10 22:26:10 -0400
  • cd842b650e Optimizing DiagnoseTargets Mauricio Carneiro 2012-04-10 09:46:29 -0400
  • 1df0adf862 Fixing ActivityProfile unit test. Ryan Poplin 2012-04-10 15:28:27 -0400
  • e3cc7cc59c Resolving merge conflict. Ryan Poplin 2012-04-10 14:50:27 -0400
  • a4634624b7 There are now three triggering options in the HaplotypeCaller. The default (mismatches, insertions, deletions, high quality soft clips), an external alleles file (from the UG for example), or extended triggers which include low quality soft clips, bad mates and unmapped mates. Added better algorithm for band pass filtering an ActivityProfile and breaking them apart when they get too big. Greatly increased the specificity of the caller by battening down the hatches on things like base quality and mapping quality thresholds for both the assembler and the likelihood function. Ryan Poplin 2012-04-10 14:48:23 -0400
  • 10e74a71eb We now allow arbitrary annotations other than dbSNP (e.g. HM3) to come out of the Unified Genotyper. This was already set up in the Variant Annotator Engine and was just a matter of hooking UG up to it. Added integration test to ensure correct behavior. Eric Banks 2012-04-10 12:30:35 -0400
  • ec9822b2a7 Revert "Disable HaplotypeCaller tests in Stable" David Roazen 2012-04-10 09:47:58 -0400
  • 2091a30b8f Merged bug fix from Stable into Unstable David Roazen 2012-04-10 09:47:40 -0400
  • bb1dff4ea4 Disable HaplotypeCaller tests in Stable David Roazen 2012-04-10 09:46:08 -0400
  • b43d21056b Merged bug fix from Stable into Unstable Mark DePristo 2012-04-10 09:42:09 -0400
  • 6885e2d065 UserException fixes for GATK_logs recent errors Mark DePristo 2012-04-10 07:37:42 -0400
  • 8507cd7440 Throw UserException for bad dict / chain files Mark DePristo 2012-04-10 07:22:43 -0400
  • cd9bf1bfc3 Changing IndelSummary eval module so that PostCallingQC.scala can run with MIXED-record VCFs. Ryan Poplin 2012-04-10 00:22:40 -0400
  • 9ece93ae9c DiagnoseTargets now outputs a VCF file Roger Zurawicki 2012-03-30 12:44:04 -0400
  • 719ec9144a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-04-09 14:53:19 -0400
  • 550179a1f7 Major refactorings/optimizations of pool caller, output still bit-true to older version: a) Move DEFAULT_PLOIDY from UnifiedGenotyperEngine to VariantContextUtils. b) Optimize iteration through all possible allele combinations. c) Don't store log PL's in hashmap from allele conformations to double, it was too slow. Things can still be optimized much more down the line if needed. d) Remove remaining traces of genotype priors. Guillermo del Angel 2012-04-09 14:53:05 -0400
  • d312fcdae8 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-04-09 14:28:49 -0400
  • f82986ee62 Adding unit tests for the very important log10sumLog10 util method. Eric Banks 2012-04-09 14:28:25 -0400
  • 63b080e353 Added index for end_time Mark DePristo 2012-04-09 14:10:53 -0400
  • ea4300d583 Refactoring so that Unified Argument Collection doesn't use deprecated classes. Eric Banks 2012-04-09 13:45:17 -0400
  • 6ddf2170b6 More efficient implementation of the sum of the allele frequency posteriors matrix using a pre-allocated cache as discussed in group meeting last week. Now, when the cache is filled, we safely collapse down to a single value in real space and put the un-re-centered log10 value back into the front of the cache. Thanks to all for the help and advice. Eric Banks 2012-04-09 11:46:16 -0400
  • 87e6bea6c1 Adding engine capability to quantize qualities. Mauricio Carneiro 2012-04-08 20:44:39 -0400
  • c055752583 Updated analyze covariates R script for new GATKReport format Mauricio Carneiro 2012-04-06 17:07:57 -0400
  • c22a66870c Modified UnitTests to respect reference padding Mark DePristo 2012-04-06 16:27:20 -0400
  • 3e29841776 Major improvements to VariantCallQC and PostCallingQC scripts Mark DePristo 2012-04-06 16:02:38 -0400
  • 45fc0ea98d Improvements to indel analysis capabilities of VariantEval Mark DePristo 2012-04-06 16:02:09 -0400
  • 52ef4a3e26 Function to compute whether a VariantContext indel is part of a TandemRepeat Mark DePristo 2012-04-06 15:58:28 -0400
  • 08fab49d30 Added function to get bases from the current base forward in the window in ReferenceContext Mark DePristo 2012-04-06 15:56:01 -0400
  • d1f2fe956f Changes to how active region triggering works around large insertions that manifest as high quality soft clips in read on one end of the insertion and low quality soft clips on the other end. The active region will now be large enough to capture the entire insertion. Need to somehow include unmapped reads with mapped mates to increase power for these events. Ryan Poplin 2012-04-06 13:17:41 -0400
  • c77104b815 Adding function call in HaplotypeCaller right before the VariantContext gets written out to disk which partitions all the reads by which allele gave the read the highest likelihood. This will allow variants to be annotated by the refactored VariantAnnotator. Uninformative reads are mapped to Allele.NO_CALL Ryan Poplin 2012-04-06 00:22:52 -0400
  • a19c27297f continuing the BQSR triage... Mauricio Carneiro 2012-04-05 10:19:52 -0400
  • 14f6b9cd16 Added two simple integration tests for pool caller with mtDNA calling - more test coverage to follow Guillermo del Angel 2012-04-05 13:06:11 -0400
  • 3561056a9c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-04-05 10:49:26 -0400
  • 5c3ddec4c2 Large refactoring of the genotyping codebase. Deprecated several of the old classes that had the wrong allele ordering and made new better copies with the correct ordering; eventually we'll push the new ones into the place of the old ones but for now we'll give users a chance to update their code. Also, removed (or deprecated as needed) the genotype priors classes since we never use them and all they serve to do is make reading the code more complicated. I expect to finish this refactoring in GATK 1.7 (or 2.0?) so that should give Kristian ample time to update. Eric Banks 2012-04-05 10:49:08 -0400
  • 7c3b3650bb BQSR bug triage Mauricio Carneiro 2012-04-04 16:40:55 -0400
  • 2c956efa53 Minor fixups to GenotypeLikelihoods Eric Banks 2012-04-05 09:14:37 -0400
  • 1e65474fec Added utility to get the reference coordinate given the read coordinate Mauricio Carneiro 2012-04-04 16:40:42 -0400
  • 82cad97caf Fix bad refactoring in previous commit: correct renaming from VariantContextUtils.assignGenotypes to VariantContextUtils.assignDiploidGenotypes Guillermo del Angel 2012-04-04 21:03:10 -0400
  • 6913710e89 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Guillermo del Angel 2012-04-04 20:17:18 -0400
  • f2aafaa3f6 More cosmetic fixes/cleanups of pool caller: use utility functions from List class instead of trying to reinvent the wheel Guillermo del Angel 2012-04-04 20:16:53 -0400
  • 76e4100d89 By default, IndelLengthHistogram won't collapse large events into the last bin, as it produces weird looking plots Mark DePristo 2012-04-04 18:36:36 -0400
  • 820216dc68 More pool caller cleanups: ove common duplicated code between Pool and Exact AF calculation models up to super-class to avoid duplication. TMP: Have pool genotypes include the GT field. Mostly because without genotypes we can't get the site-wide AF,AC annotations, but it's unwieldy because it makes the genotype columns very long, TBD final implementation Guillermo del Angel 2012-04-04 16:23:10 -0400
  • bfad26353a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-04-04 16:04:50 -0400
  • dda2173c66 Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned. Ryan Poplin 2012-04-04 16:04:29 -0400