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  • 2311606de4 initial cancer pipeline with mutations and partial indel support Kristian Cibulskis 2012-10-03 16:25:34 -0400
  • 45aa59a31c BAM pipeline fixes: a) temp workaround for DEV-9: -nWayOut argument in IndelRealigner is broken, for now things will only really work in single sample mode, b) correct extension of RealignerTargetCreator output, previous extension caused an error Guillermo del Angel 2012-10-04 10:53:13 -0400
  • b8c721e6ec Minor tweaks to CMIProcessing Pipeline: a) don't hard-code job mem limit to 4 G since it's too much for most AWS instances, leave it instead as input argument, b) minor doc cleanups Guillermo del Angel 2012-10-03 12:05:57 -0400
  • ca055d8804 Reimplementation of the BAM procesing pipeline using the metadata information file. Mauricio Carneiro 2012-10-02 12:48:55 -0400
  • 25ff934e5a New version of the pipeline starting from an ALIGNED bam going all the way to reducing using n-way out cleaning Mauricio Carneiro 2012-09-26 16:16:53 -0400
  • 7d4adea183 Revised implementation of the RAWBAM => BAM pipeline Mauricio Carneiro 2012-09-26 13:37:15 -0400
  • e413b9fe51 First implementation of the CMI data processing pipeline, handling both germline and cancer BAM/FQ => BAM. Mauricio Carneiro 2012-09-25 17:15:42 -0400
  • 0c17709223 First implementation of a generic 'bundled' Data Processing Pipeline for germline and cancer. Mauricio Carneiro 2012-09-25 17:13:50 -0400
  • 08b6d1559c Reverting the DPP to the original version, going to create a new simplified version for CMI in private. Mauricio Carneiro 2012-09-25 12:02:34 -0400
  • f9095c7ab7 Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it) Mauricio Carneiro 2012-09-24 17:01:17 -0400
  • 15b405d458 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ryan Poplin 2012-10-10 10:47:40 -0400
  • 2a9ee89c19 Turning on allele trimming for the haplotype caller. Ryan Poplin 2012-10-10 10:47:26 -0400
  • 7381d5c243 Since this GRM now matches GCTA output for uncorrected intervals, implement and start proofing methods for LD-correction for genome partitioning. Very rudimentary tests just to solidify current position. Christopher Hartl 2012-10-10 01:59:13 -0400
  • f66284658d RetryMemoryLimit now works with Scatter/Gather. Khalid Shakir 2012-10-09 18:31:56 -0400
  • e9b9e2318c Fixed SortSam bug, for .done file Johan Dahlberg 2012-10-03 11:35:43 +0200
  • 9d7aa3cda8 a) Initial raw version of CMI BAM->VCF pipeline (most likely not working yet, but at least compiles and produces reasonable command lines), b) rename FASTQ->BAM script so name is more descriptive Guillermo del Angel 2012-10-09 11:45:24 -0400
  • b543bddbb7 Fixing merge conflicts related to the comment formatting in the BQSR. Ryan Poplin 2012-10-08 10:23:08 -0400
  • b3cc04976f Fixing BQSR bug reported on the forum for reads that being with insertions. Ryan Poplin 2012-10-08 10:18:29 -0400
  • be9fcba546 Don't allow triggering of polyploid consensus creation in regions where there is more than one het, as it just doesn't work properly. We could probably refactor at some point to make it work, but it's not worth doing that now (especially as it should be rare to have multiple proximal known hets in a single sample exome). Eric Banks 2012-10-07 16:32:48 -0400
  • 08ac80c080 RR bug: when the last base in the window around the polyploid consensus is filtered (low quality), the filtered consensus is not flushed and subsequent filtered bases (but importantly not contiguous to this one) are just added to this position. In other words, bases were being added to the wrong genomic positions. Fixed. Eric Banks 2012-10-07 10:52:01 -0400
  • 36a26a7da6 md5s failed because I forgot to add --no_cmdline_in_header so it is different depending on where you run from. Fixed. Eric Banks 2012-10-07 08:35:55 -0400
  • a5aaa14aaa Fix for GSA-601: Indels dropped during liftover. This was a true bug that was an effect of the switch over to the non-null representation of alleles in the VariantContext. Unfortunately, this tool didn't have integration tests - but it does now. Eric Banks 2012-10-07 01:19:52 -0400
  • 82e40340c0 Use StringBuilder over StringBuffer Eric Banks 2012-10-07 00:02:15 -0400
  • 5d6aad67e2 Fix for bug reported on forums: VariantsToTable does not handle lists and nested arrays correctly. Added an integration test to cover printing of PLs. Eric Banks 2012-10-07 00:01:27 -0400
  • e7798ddd2a Fix for JIRA GSA-598: AD field not handled properly by CombineVariants. It was also not handled by SelectVariants either. We now strip the AD field out whenever combining/selecting makes it invalid due to a changing of the number of ALT alleles. Eric Banks 2012-10-06 23:02:36 -0400
  • bfc551f612 Fix for GSA-589: SelectVariants with -number gives biased results. The implementation was not good and it's not worth keeping this busted code around given that we have a working implementation of a fractional random sampling already in place, so I removed it. Eric Banks 2012-10-06 22:39:49 -0400
  • e8a6460a33 After merging with Yossi's fix I can confirm that the AD is fixed when going through the HC too. Added similar fixes to DP and FS annotations too. Eric Banks 2012-10-05 16:37:42 -0400
  • b7639d7ceb Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-10-05 16:21:17 -0400
  • 52326942cf Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-10-05 16:15:07 -0400
  • 04853252a0 Possible fix for reduced reads coming from the HaplotypeCaller in the AD Eric Banks 2012-10-05 16:15:04 -0400
  • ef90beb827 - forgot to use git rm to delete a file from git. Now that VCF is deleted. - uncommented a HC test that I missed. Yossi Farjoun 2012-10-05 16:14:51 -0400
  • 6874a5ce76 This bam and bai are needed for testing the ADAnnotation tests (both UG and HC) The vcf file was mistakenly added previously, now removed. Yossi Farjoun 2012-10-05 16:10:41 -0400
  • d419a33ed1 * Added an integration test for AD annotation in the Haplotype caller. * Corrected FS Anotation for UG as for AD. * HC still does not annotate ReducedReads correctly (for FS nor AD) Yossi Farjoun 2012-10-05 15:23:59 -0400
  • dc4dcb4140 fixed AD annotation for a ReducedReads BAM file. Added an integration test for this case with a new reduced BAM in private/testdata Yossi Farjoun 2012-10-05 14:20:07 -0400
  • f840d9edbd HC test should continue using 3 alt alleles for indels Eric Banks 2012-10-05 02:03:34 -0400
  • c66ef17cd0 Add a separate max alt alleles argument for indels that defaults to 2 instead of 3. PLEASE TAKE NOTE. Eric Banks 2012-10-04 13:52:14 -0400
  • beaa1ac07e Turns out GCTA replaces a missing variant with the mean dosage (2*frequency), but then normalizes the genetic distance by the number of non-missing genotype pairs. An odd thing to do, but with this the GRMs are confluent (up to a small tolerance) Christopher Hartl 2012-10-04 13:29:38 -0400
  • 01dcdf2830 Waypoint: GRM is identical with GCTA if no genotypes are missing. Not sure how GCTA is treating these, but it's definitely not strictly excluding them. Christopher Hartl 2012-10-04 12:53:03 -0400
  • 3ffba77656 Revert "initial cancer pipeline with mutations and partial indel support" Scott Frazer 2012-10-04 11:37:54 -0400
  • 0afde9906a initial cancer pipeline with mutations and partial indel support Kristian Cibulskis 2012-10-03 16:25:34 -0400
  • e13e61673b Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-10-04 10:54:23 -0400
  • 49db96c8ad BAM pipeline fixes: a) temp workaround for DEV-9: -nWayOut argument in IndelRealigner is broken, for now things will only really work in single sample mode, b) correct extension of RealignerTargetCreator output, previous extension caused an error Guillermo del Angel 2012-10-04 10:53:13 -0400
  • dfddc4bb0e Protect against cases where there are counts but no quals Eric Banks 2012-10-04 10:52:30 -0400
  • 0c46845c92 Refactored the BaseCounts classes so that they are safer and allow for calculations on the most probable base (which is not necessarily the most common base). Eric Banks 2012-10-04 10:37:11 -0400
  • b6e20e083a Copied DiploidExactAFCalc to placeholder OptimizedDiploidExact Mark DePristo 2012-10-03 20:16:38 -0700
  • 51cafa73e6 Removing public -> private dependency Mark DePristo 2012-10-03 20:05:03 -0700
  • f6a2ca6e7f Fixes / TODOs for meaningful results with AFCalculationResult Mark DePristo 2012-10-03 19:54:27 -0700
  • 50e4a832ea Generalize framework for evaluating the performance and scaling of the ExactAF models to tri-allelic variants Mark DePristo 2012-10-02 19:17:37 -0500
  • 3663fe1555 Framework for evaluating the performance and scaling of the ExactAF models Mark DePristo 2012-10-02 16:27:09 -0500
  • 17ca543937 More ExactModel cleanup Mark DePristo 2012-10-02 08:39:51 -0500
  • f8ef4332de Count the number of evaluations in AFResult; expand unit tests Mark DePristo 2012-10-01 14:14:44 -0500
  • 33c7841c4d Add tests for non-informative samples in ExactAFCalculationModel Mark DePristo 2012-10-01 13:03:08 -0500
  • de941ddbbe Cleanup Exact model, better unit tests Mark DePristo 2012-09-30 20:21:18 -0400
  • 3e01a76590 Clean up AlleleFrequencyCalculation classes Mark DePristo 2012-09-30 17:56:54 -0400
  • 1c52db4cdd Add exactCallsLog output file to ExactModel and StandardCallerArgumentCollection Mark DePristo 2012-09-30 11:34:32 -0400
  • ca31ddf2a5 Allow VCFs without PLs to be converted to a bed file with genotypes other than no-call (by setting the minimum GQ to <=0). Performance enhancements to GRM suite. Christopher Hartl 2012-10-03 21:36:35 -0400
  • dca7c7fa9c initial cancer pipeline with mutations and partial indel support Kristian Cibulskis 2012-10-03 16:25:34 -0400
  • 1be8a88909 Changes: 1) GATKArgumentCollection has a command to turn off randomization if setting the seed isn't enough. Right now it's only hooked into RankSumTest. 2) RankSumTest now can be passed a boolean telling it whether to use a dithering or non-randomizing comparator. Unit tested. 3) VariantsToBinaryPed can now output in both individual-major and SNP-major mode. Integration test. 4) Updates to PlinkBed-handling python scripts and utilities. 5) Tool for calculating (LD-corrected) GRMs put under version control. This is analysis for T2D, but I don't want to lose it should something happen to my computer. Christopher Hartl 2012-10-03 16:02:42 -0400
  • 9e1592b8ba Minor tweaks to CMIProcessing Pipeline: a) don't hard-code job mem limit to 4 G since it's too much for most AWS instances, leave it instead as input argument, b) minor doc cleanups Guillermo del Angel 2012-10-03 12:05:57 -0400
  • 118e974731 GATK Engine: special-case "monolithic" FilePointers, and allow them to represent multiple contigs David Roazen 2012-10-02 15:17:58 -0400
  • 7660e9f820 Reimplementation of the BAM procesing pipeline using the metadata information file. Mauricio Carneiro 2012-10-02 12:48:55 -0400
  • a96ed385df ReadShard.getReadsSpan(): handle case where shard contains only unmapped mates David Roazen 2012-10-02 13:43:01 -0400
  • 9a8f53e76c Probably the GATK's most seen typo in the world Mauricio Carneiro 2012-10-02 13:34:37 -0400
  • ac87ed47bb BQSR: allow logging recal table updates to a file David Roazen 2012-10-01 13:54:26 -0400
  • 2508b0f5a7 Merged bug fix from Stable into Unstable Christopher Hartl 2012-09-29 00:57:43 -0400
  • 365f1d2429 hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items: 1) ValidateVariants removed in favor of direct validation VariantContexts. Integration test added to test broken contexts. 2) Enabling indel and SV output. Still bi-allelic sites only. Integration tests added for these cases. 3) Found a bug where GQ recalculation (if a genotype has PLs but no GQ) would only happen for flipped encoding. Fixed. Integration test added. Christopher Hartl 2012-09-29 00:55:31 -0400
  • 11540da98b Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ami Levy Moonshine 2012-09-28 21:01:25 -0400
  • 2df5be702c Added an argument to RR to allow polyploid consensus creation (by default it is turned off). This will eventually be replaced by the known SNPs track trigger. Eric Banks 2012-09-28 11:44:25 -0400
  • fb9457d6fe Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Ami Levy Moonshine 2012-09-27 22:40:39 -0400
  • e740977994 GATK Engine: do not merge FilePointers that span multiple contigs David Roazen 2012-09-27 17:59:02 -0400
  • e82946e5c9 ExperimentalReadShardBalancer: create one monolithic FilePointer per contig David Roazen 2012-09-25 11:37:17 -0400
  • a640afa995 adding some directories to gitignore Mauricio Carneiro 2012-09-27 11:09:41 -0400
  • 3e68fee764 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) Mauricio Carneiro 2012-09-27 11:04:56 -0400
  • abbe757907 Merged bug fix from Stable into Unstable Christopher Hartl 2012-09-27 00:15:35 -0400
  • 55cdf4f9b7 Commit changes in Variants To Binary Ped to the stable repository to be available prior to next release. Christopher Hartl 2012-09-27 00:13:32 -0400
  • b9dab068ee New version of the pipeline starting from an ALIGNED bam going all the way to reducing using n-way out cleaning Mauricio Carneiro 2012-09-26 16:16:53 -0400
  • f8b954334e Revised implementation of the RAWBAM => BAM pipeline Mauricio Carneiro 2012-09-26 13:37:15 -0400
  • 33b2f65bbd Script to evaluate SNP and indel calls for the experimental downsampler Mark DePristo 2012-09-26 11:18:40 -0400
  • f009424952 Adding Phase2 HC calling qscripts for both the original calls and the project consensus. Ryan Poplin 2012-09-26 11:26:24 -0400
  • e49fe74612 Adding some of the qscripts from my BQSR experiments. Ryan Poplin 2012-09-26 10:55:34 -0400
  • c9c2682f86 removing annoying xml from IDEA configuration Mauricio Carneiro 2012-09-25 17:18:44 -0400
  • 9486131d17 First implementation of the CMI data processing pipeline, handling both germline and cancer BAM/FQ => BAM. Mauricio Carneiro 2012-09-25 17:15:42 -0400
  • cb8d4c97e1 First implementation of a generic 'bundled' Data Processing Pipeline for germline and cancer. Mauricio Carneiro 2012-09-25 17:13:50 -0400
  • 65b100f9b0 Reverting the DPP to the original version, going to create a new simplified version for CMI in private. Mauricio Carneiro 2012-09-25 12:02:34 -0400
  • 4324bd72fd Updating Intellij enviroment and adding Scala Mauricio Carneiro 2012-09-25 10:51:53 -0400
  • e1524ebbc8 NA12878 HiSeq b37 20:10-11 mb test files Mark DePristo 2012-09-25 08:53:44 -0400
  • caa431c367 Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable Eric Banks 2012-09-24 21:46:36 -0400
  • 11a71e0390 RR bug: when determining the most common base at a position, break ties by which base has the highest sum of base qualities. Otherwise, sites with 1 Q2 N and 1 Q30 C are ending up as Ns in the consensus. I think perhaps we don't even care about which base has the most observations - it should just be determined by which has the highest sum of base qualities - but I'm not sure that's what users would expect. Eric Banks 2012-09-24 21:46:14 -0400
  • 4aad135f8c Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it) Mauricio Carneiro 2012-09-24 17:01:17 -0400
  • ca84586443 Adding default intellij configuration files Mauricio Carneiro 2012-09-24 16:15:57 -0400
  • 3f44b3e019 Update DataProcessingPipelineTest MD5s David Roazen 2012-09-24 15:38:07 -0400
  • 0b488cce66 ExperimentalReadShardBalancer: close() exhausted iterators David Roazen 2012-09-24 14:45:53 -0400
  • 9fd30d6f1c When writing the initial commit for nt + nct I realized this class was really just a ThreadGroupOutputTracker Mark DePristo 2012-09-23 18:19:10 -0400
  • 3e8d992828 Remove bad error test from MicroScheduler, as it's no longer applicable. Mark DePristo 2012-09-23 18:13:44 -0400
  • a6b3497eac Fixes GSA-515 Nanoscheduler GSA-577 -nt and -nct together appear to not close resources properly Mark DePristo 2012-09-23 18:02:48 -0400
  • 4749fc114f Temp. disable -nt > 1 and -nct > 1 while bugs are worked out Mark DePristo 2012-09-22 16:22:42 -0400
  • 847e79247d Use SNP only model for NCT big exome test Mark DePristo 2012-09-22 16:19:28 -0400
  • f42e55c9df Add NCT specific performance test for 5K exomes Mark DePristo 2012-09-22 13:44:42 -0400
  • 09bbd2c4c3 Include exception in VCFWriter when one is found when rethrowing as ReviewedStingException Mark DePristo 2012-09-22 13:22:27 -0400
  • 10a6b57be6 Fix thread name: should be master executor not input Mark DePristo 2012-09-22 13:21:55 -0400