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  • c1e09efb23 - Fixed output for beagle header - Better description for QualByDepth annotation ebanks 2010-01-21 21:25:56 +0000
  • d9df72e1b5 AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value. rpoplin 2010-01-21 21:15:11 +0000
  • 4fc926232c More cleanup. Make sure resources are unioned among all the specified modules. hanna 2010-01-21 19:38:46 +0000
  • 3e54e131e0 Cleanup and formatting overhaul. hanna 2010-01-21 19:22:56 +0000
  • ee421c106c Autogenerate .tar.bz2 with embedded version number. Misc formatting changes. hanna 2010-01-21 18:32:46 +0000
  • f51cffe220 Alteration of PlinkToVCF to be much more flexible about parsing .ped file headers, which can have one of a number of different standard fields, and be in different orders. chartl 2010-01-21 18:02:28 +0000
  • 5b2a1e483e Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly. chartl 2010-01-21 17:35:20 +0000
  • 74779a9a78 First version of the tool that tries determining indel error rate (basically, counts indels that look like sequencing/alignment errors - such as a single observation at deeply covered locus, and reports the rate of their occurence) asivache 2010-01-21 15:28:20 +0000
  • d25a2fe120 Better handling of enums by the command-line argument system. hanna 2010-01-20 21:36:46 +0000
  • 9c7b281b4f Set default value for max_coverage to be 100K (since 10K is too small). ebanks 2010-01-20 20:15:25 +0000
  • 1e9fe2a334 Clean up error output when enums have missing arguments. hanna 2010-01-20 19:48:26 +0000
  • 8d1d37302c a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output. aaron 2010-01-20 19:36:49 +0000
  • 908d399670 Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built. hanna 2010-01-20 19:18:19 +0000
  • ab289872e4 Changes: chartl 2010-01-20 16:45:17 +0000
  • cf46e3c85f Valuable series of commands depristo 2010-01-20 13:58:59 +0000
  • a1b4cc4baf changes to intelligently log overflowing locus pile-ups. aaron 2010-01-20 08:09:48 +0000
  • 4ac9eb7cb2 - Smarter strand bias calculation - Better debug/verbose printing ebanks 2010-01-20 03:01:26 +0000
  • 2261f57e5c Rename modules to reflect the fact that they're really packages in their own right. hanna 2010-01-20 01:13:17 +0000
  • 2f3fbc145d A rethink of some of the modules from last night -- make the modules stand alone. hanna 2010-01-20 00:59:21 +0000
  • ff66023d83 Trivial change to support filter field in VCF depristo 2010-01-19 22:56:22 +0000
  • 4625261d79 Bug fix: alignments ending with 'I' were not counted into the overall coverage which resulted in inaccurate stats, and in rare occasions outright messed up ones. asivache 2010-01-19 22:12:16 +0000
  • 96a053c769 Port VariantEval and FindContaminatingReadGroups to modules. hanna 2010-01-19 22:10:33 +0000
  • 8dafd26100 Print out the current version number in the application header. hanna 2010-01-19 21:58:36 +0000
  • 9e0ae993c7 -B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%) depristo 2010-01-19 21:33:13 +0000
  • e936cbff1b Removed experimental recalibration covariates. kshakir 2010-01-19 21:29:43 +0000
  • c98df0a862 Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen. rpoplin 2010-01-19 21:18:02 +0000
  • 53352e1bb4 First pass at a sequenom ROD. Nothing uses it; currently undergoing testing. chartl 2010-01-19 17:09:36 +0000
  • 1488578617 Working with Aaron to get svnversion running within the build system. This change will break the build. hanna 2010-01-19 16:55:42 +0000
  • bca436578f Added the -maxQ argument to the list of arguments in the PG tag rpoplin 2010-01-19 15:55:23 +0000
  • d61cafd19f Make the formatting of the list of args in the PG tag consistent. rpoplin 2010-01-19 15:31:37 +0000
  • a12465b6d5 The recalFile argument is no longer added into the PG tag of a bam produced by TableRecalibration. Based on a request from the Sanger. rpoplin 2010-01-19 15:25:57 +0000
  • e1fba42fdb Add new 'module' XML tag, that can import modules from supplementary files. hanna 2010-01-19 01:56:04 +0000
  • ba19afd529 Draft version of AnalyzeAnnotations which creates plots of cumulative TiTv ratio versus filter value per each annotation in the input VCF rod. Minor cleanup of recalibration walkers. rpoplin 2010-01-18 20:47:10 +0000
  • ff6877a15e Added a forgotten column label kiran 2010-01-18 01:00:52 +0000
  • dd6d5aadf9 Computes empirical confusion matrices, optionally with up to five bases of preceding context kiran 2010-01-18 00:55:12 +0000
  • 12453fa163 Misc cleanup of UG args ebanks 2010-01-17 04:38:52 +0000
  • a57886ab81 Adding VCFValidator to package ebanks 2010-01-17 03:39:05 +0000
  • b8cdf64c20 Better descriptions for max reads/downsampling args ebanks 2010-01-17 02:30:27 +0000
  • aa08c82ac0 Removed experimental covariates and added standard annotations. ebanks 2010-01-17 02:17:32 +0000
  • 8226f4aa12 minor cleanup depristo 2010-01-16 20:23:20 +0000
  • d8e74c5795 Update to MD5s for old tests and added extensive VCF testing depristo 2010-01-16 20:22:58 +0000
  • 64225b28fd Convenience methods for getting the VCFReader and VCFRecord depristo 2010-01-16 20:22:31 +0000
  • d0af7f6c7b Now analyzes filtered SNP like all, novel subsets; support for selecting a single sample to analyze from a multi-sample VCF, support for trivial selection of records with INFO field key/value pair. depristo 2010-01-16 20:22:04 +0000
  • 8ae8e120f8 New annotateUnion operation -- provides clearer annotations on where a call came from when unioning two VCF call sets depristo 2010-01-16 20:20:37 +0000
  • 41392f8ff5 functions for setting gentoype records and alternate bases; function for getting all rods implementing VCF depristo 2010-01-16 20:19:43 +0000
  • d2961a3a17 Typo in previous commit. hanna 2010-01-16 01:41:42 +0000
  • 45de006ca3 Disable extraction of svn info completely. hanna 2010-01-16 01:30:25 +0000
  • 8ce79e002c Fix for failed build. Seems to be an issue with Bamboo environment. I'll discuss w/ Aaron next week. hanna 2010-01-16 01:06:26 +0000
  • ac4756db20 Add the svn version on the fly to the version number properties. hanna 2010-01-16 00:28:01 +0000
  • 420cef4094 Added version numbers to the help doclet extractor. Since the help system is behaving more like a resource bundle at this point, changed it over to use the Java ResourceBundle support classes. hanna 2010-01-15 23:31:29 +0000
  • 4de7d6a59b Initial checkin of skeleton code for AnalyzeAnnotations rpoplin 2010-01-15 21:52:34 +0000
  • 930082314a Put a major.minor version into the GATK Javadoc for reading. Also, update some straggler packages to the new package-info.java format introduced in 1.5. hanna 2010-01-15 21:48:30 +0000
  • 3063224446 SecondaryBaseTransitionTableWalker now breaks by genotype and read group, is javadoc annotated, and is compatible with ReadBackedPileup's methods. mmelgar 2010-01-15 21:43:39 +0000
  • d30e2b390a Remove several walkers that won't be used in the GATK-GSA-Pipeline.jar. kshakir 2010-01-15 21:17:23 +0000
  • 7a991421f7 -erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) asivache 2010-01-15 21:11:14 +0000
  • c8c5c176cd -erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) asivache 2010-01-15 21:07:49 +0000
  • a12933a26d Bug fixed: now the length of an insertion is determined correctly. Thought I committed this... asivache 2010-01-15 20:58:48 +0000
  • d2f752dbc1 Adding TileCovariate to the GATK-GSA-Pipeline list. rpoplin 2010-01-15 20:57:13 +0000
  • 190335db9c Added a GSA specific package with Playground walkers. kshakir 2010-01-15 20:50:29 +0000
  • 404b95183f This is a LocusWalker, not a RodWalker (thanks Mark!!). RodWalkers currently are not capable of attaching alignment contexts (reads) to the ROD-annotated loci they traverse over... asivache 2010-01-15 20:33:41 +0000
  • 7078219b89 Updating outdated comments. rpoplin 2010-01-15 19:17:52 +0000
  • ba2acda406 Clarifying the comment regarding differentiating between first and second of pair in CycleCovariate. rpoplin 2010-01-15 18:36:14 +0000
  • b911b7df82 Fixing the AC annotation to be in line with the VCF spec ebanks 2010-01-15 18:28:52 +0000
  • f2e539c52f As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely. rpoplin 2010-01-15 18:18:59 +0000
  • eae1b73945 Fixed a bug in left-adjusting the indels introduced in previous commit :-/ asivache 2010-01-15 17:41:23 +0000
  • df998041a8 Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file. rpoplin 2010-01-15 16:31:25 +0000
  • 70df30fc1b Added method to AlignmentUtils which takes a read's cigar and the refBases char array given to a ReadWalker and returns the aligned reference char array. Bug fix in solid_recal_modes to use this aligned reference array. Recalibrator version number is no longer separate for each of the two walkers. rpoplin 2010-01-15 15:36:59 +0000
  • 2a116bb5d6 Made the VCF validator a simple rod walker instead of having it be in a separate package. ebanks 2010-01-15 06:39:06 +0000
  • b19bb19f3d First successful test of new sharding system prototype. Can traverse over reads from a single BAM file. hanna 2010-01-15 03:35:55 +0000
  • db9570ae29 Looks bigger than it is: aaron 2010-01-15 00:14:35 +0000
  • cff8b705c0 Oh, and the test would not work anymore... asivache 2010-01-14 17:47:09 +0000
  • 04fdbbfa65 This is the beginning of a new version of VariantEval that can cut VCF files up in a variety of ways with JEXL expressions, select one sample out of a multi-sample VCF, and can load analysis modules dynamically. kiran 2010-01-14 17:45:58 +0000
  • df63f51253 No changes, just sync-ing; only some commented out debugging prints are added... asivache 2010-01-14 17:45:15 +0000
  • d85461c463 MergingIterator completely re-done. Now it is not a generic class (sorry guys), but rather it is tailored for merging ROD tracks. This implementation peeks the locations of next ROD annotations in each track, but does not actually read these RODs from underlying streams until the location is reached and it is time to actually return the object. Now underlying ROD track iterators (registered in the resource pool!) are not advanced prematurely past the current position and all the way to the next ROD record wherever it is, so that the sharding system can reuse them. asivache 2010-01-14 17:43:36 +0000
  • c0891d512f added: peekNextLocation(); it's quite hard (and probably unnecessary, ever) to make seekable iterator a peekable one, but it is quite easy and useful to be able to peek just the next location the iterator will jump to after next call to next() asivache 2010-01-14 17:38:19 +0000
  • 9bf0d7250a Fixing the testOtherOutput UG integration test so it will run. rpoplin 2010-01-14 13:40:14 +0000
  • a082b948a3 Support throughout for S and N cigar elements. ebanks 2010-01-14 03:45:42 +0000
  • 9f89c62c75 Added b37 reference files and dbsnp 130 rods to resources ebanks 2010-01-14 03:28:22 +0000
  • 424d1b57f7 Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF chartl 2010-01-13 23:22:37 +0000
  • f96b2b211e My last checkin updating R code broke an unrelated UnifiedGenotyper integration test. Eric says that I should take out the verbose test. rpoplin 2010-01-13 22:28:10 +0000
  • 7f97041875 Update to AnalyzeCovariates to make the histogram of PairedReadOrder look a little nicer rpoplin 2010-01-13 20:26:31 +0000
  • 49c44e7b36 PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests. rpoplin 2010-01-13 20:09:10 +0000
  • 05575e2e56 Better bounding for the locus window. Don't make the locus window calculation blow up if the GenomeLoc ends up being outside the reference. Force the blowup elsewhere. hanna 2010-01-13 17:03:54 +0000
  • 8ca5bba738 We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test). SequenomToVCF now correctly has no-calls when probes fail. Re-enabled SequenomToVCF integration test. ebanks 2010-01-13 15:40:27 +0000
  • 6d1107a4ed Update to SequenomToVCF chartl 2010-01-13 15:32:05 +0000
  • f99586f91b Added integration test for beagle and verbose output in UG. Minor cleanup of VCFRecord code. ebanks 2010-01-13 03:55:24 +0000
  • 02e23e2d9c Threading support for beagle output files. hanna 2010-01-13 02:42:16 +0000
  • 0513690416 two fixes in the new cached DbSNP code: -isBiallelic would incorrectly say triallelic sites are biallelic. -getAlternateAlleleList was broken, since the new cached list is immutable, we couldn’t remove list items. aaron 2010-01-13 00:27:34 +0000
  • a138bad95a A rare but not-so-subtle bug fixed: a funky alignment (a kind that should not have been generated in the first place) could make the indel left-adjusting method to overshoot read start and build a cigar like -3M6I... also, few minor fix-ups. asivache 2010-01-12 21:29:50 +0000
  • b51f4aae11 Updating the recalibrator to make use of StingSAMFileWriter. rpoplin 2010-01-12 20:58:27 +0000
  • c8ad025ad0 cleaning up unused import statements rpoplin 2010-01-12 18:52:37 +0000
  • 189829841b The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two. rpoplin 2010-01-12 18:50:39 +0000
  • 16777e3875 more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode). aaron 2010-01-12 18:47:43 +0000
  • 35a4fcc481 Additional sanity checking: make sure the user can't alter the header / compression level / presorted state of a file to which SAMRecords have already been written. hanna 2010-01-12 18:39:41 +0000
  • 03b7d5f5c7 1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation. ebanks 2010-01-12 18:33:53 +0000
  • 58999a8e9d Enhance the I/O management system to support custom headers and set the presorted flag from the initialize() method (or at any time before the first SAM record is written). hanna 2010-01-12 18:21:42 +0000
  • 3c5f5177b1 check to see if the parsed interval list is empty, since we now allow interval files that are empty. If so, make sure we default to a non-interval based traversal. aaron 2010-01-12 17:52:27 +0000
  • 040fdfee61 Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter. I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF. ebanks 2010-01-11 21:42:12 +0000
  • 3feead019d New Picard and SAM-JDK with automatic sequence name truncation alecw 2010-01-11 20:49:13 +0000
  • 42aff1d2c3 Annotator in general should be able to annotate monomorphic or tri-allelic sites. It's up to the individual annotations to decide whether they want to annotate or not. ebanks 2010-01-11 19:52:18 +0000