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Author SHA1 Message Date
delangel 55b756f1cc First step in major cleanup/redo of VCF functionality. Specifically, now: 
a) VCF track name can work again with 3.3 or 4.0 VCF's when specifying -B name,VCF,file. Code will read header and parse automatically the version. 
b) Old VCF codec is deprecated. Reader goes now direct from parsing VCF lines into producing VariantContext objects, with no intermediate VCF records. If anyone can't resist the urge to still input files using the old method, a new VCF3Codec is in place with the old code, but it will be eventually deleted.
c) VCF headers and VCF info fields no longer keep track of the version. They are parsed into an internal representation and will be output only in VCF4.0 format.
d) As a consequence, the existing GATK bug where files are produced with VCF4 body but VCF3.3 headers is solved.
e) Several VCF 4.0 writer bugs are now solved.
f) Integration test MD5's are changed, mostly because of corrected VCF4.0 headers and because validation data mostly uses now VCF4.0.
g) Several VCF files in the ValidationData/ directory have been converted to VCF 4.0 format. I kept the old versions, and the new versions have a .vcf4 extension.

Pending issues:
a) We are still not dealing with indels consistently or correctly when representing them. This will be a second part of the changes.
b) The VCF writer doesn't use VCFRecord but it does still use a lot of leftovers like VCFGenotypeEncoding, VCFGenotypeRecord, etc. This needs to be simplified and cleaned.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3813 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 22:49:16 +00:00
aaron 36ac73cf9a comment out broken test until it can be fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3810 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 20:04:40 +00:00
depristo b29eda83bb Parallelized CountCovarites! percent_ref_called_var now a standard genotype concordance module (for validation!). Really much smarter merging of headers for combineVariants. VCF codecs now actually look at the file version and blow up if they are the wrong versions. setHeaderVersion() in VCFHeaderLine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3802 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 14:10:18 +00:00
ebanks e7e58d7129 The SAM spec has now officially reserved my new tags for original cigar and original alignment start... except that OS has been named OP ('original POS') 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3800 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 00:09:36 +00:00
ebanks a4f8d70d8d oops, forgot to update this integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3788 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-14 11:38:33 +00:00
ebanks 460283f6d2 No more manually converting VariantContexts to VCFRecords. You should be utilizing VCs and not VCFRecords. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3787 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-14 05:21:28 +00:00
ebanks 6b5c88d4d6 The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3786 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-14 04:56:58 +00:00
ebanks d896d03554 Moving VF to vcf 4.0. Still need to fix genotype filters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3777 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 11:39:51 +00:00
ebanks 76b3b39720 Technically, Mark broke this with his commit earlier. But since I had an outstanding broken test, I lose and have to fix this one too... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3776 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 03:58:38 +00:00
ebanks 1bef7dd170 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3775 348d0f76-0448-11de-a6fe-93d51630548a 2010-07-13 00:56:12 +00:00
ebanks 52c534a8f2 Updating to VCF 4.0 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3770 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 20:18:30 +00:00
ebanks e50627a49e 1. Updated tests and added integration test for liftover code. 
2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 17:58:18 +00:00
ebanks 221e01fb27 deleting/archiving as instructed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3765 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 16:59:45 +00:00
ebanks fb717fe128 First pass needed to remove old VCF code: moving all VCF-related constants into a single unified class 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3759 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-11 07:19:16 +00:00
chartl ea8fd506bf Update to PickSequenomProbes: Option to ignore mask sites within X bp of a variant (very useful for indels where dbSNP entries near the indel are almost always false SNP calls). Also fixed an integration test where the variant site itself, being in dbSNP, was represented as [N/C] rather than [A/C]. Added integration test for 1bp no-mask window. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3753 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-09 04:03:19 +00:00
depristo 45fb614296 Fixes to VE for obscure bug, as well as disabled integration test for CombineVariants 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3749 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-09 00:13:07 +00:00
ebanks 6e6ad36523 reallow MNP events through 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3740 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-08 06:26:52 +00:00
ebanks 9a81f1d7ef Fixed this tool for chartl so that it now properly handles deletions. Added deletion case to integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3737 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-08 04:45:59 +00:00
hanna 9fc05ac2ae eagerDecode is now false. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3733 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 22:51:48 +00:00
ebanks 4bc3ad2194 Shame on me: UG was emitting negative QUALs (-0) in all_bases mode. Thanks, Matt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3732 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 20:30:22 +00:00
ebanks 30714ec8d9 As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3731 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 20:12:59 +00:00
aaron 86031f4034 part two: todo's in combine variants, fixes for InferredGeneticContext, and some other tests and clean-up. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3721 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 21:07:53 +00:00
ebanks 36edc60ccc Connected UG to the new comp track annotation system in VA. Also, when emit confidence is lower than call confidence (so that we emit records filtered with LowQual), add a corresponding FILTER header field to the VCF so that the validator doesn't complain. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3720 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 13:04:24 +00:00
rpoplin 255b036fb5 Variant Recalibrator MLE EM algorithm is moved over to variational Bayes EM in order to eliminate problems with singularities when clustering in higher than two dimensions. Because of this there is no longer a number of Gaussians parameter. Wiki will be updated shortly with new recommended command. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3704 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 18:51:07 +00:00
ebanks 944dbb94ce Refactored and generalized the database/comp annotations in VariantAnnotator. Now one can provide comp tracks as with VariantEval (e.g. compHapMap, comp1KG_CEU) and the INFO field will be annotated with the track name (without the 'comp') if the variant record overlaps a comp site (e.g. ...;1KG_CEU;...). This means that you can now pass 1kg calls to the Unified Genotyper and automatically have records annotated with their presence in 1kg. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3684 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 16:37:31 +00:00
ebanks 12c0de6170 Added ability to clean using only known indels. Added integration test for it. Fixed vcf->vc conversion for indels which was busted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3678 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 01:20:56 +00:00
ebanks baf9479c35 An addition for Sendu since he can't seem to tell when his CountCovariate jobs die in the middle of writing the CSVs. We now write an EOF marker at the end of the covariates table and look for it when reading in the file in TableRecalibrationWalker. By default, we warn the user if the EOF marker isn't present, but we exception out if the user provides the --fail_with_no_eof_marker option. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3670 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 18:50:07 +00:00
ebanks 4a451949ba add parallel option to target creator for masking out reads with bad mates 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3663 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 22:13:25 +00:00
ebanks 6a23edd911 Fix performance tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3662 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 21:51:48 +00:00
ebanks 1292c96e29 The cleaner now adds the OC (original cigar) and OS (original alignment start) tags as appropriate to reads that get realigned; this feature can be turned off. Also, improved integration tests (sorry, Kiran!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3657 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 16:46:47 +00:00
ebanks bf5cbad04c Make the target creator a rod walker (that allows reads) so that we can easily trigger the cleaner on only known indel sites. Adding an integration test to cover this case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3651 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 13:28:37 +00:00
ebanks 8e848ccd84 SAMFileWriters can now write to /dev/null without throwing exceptions, so we can remove the try/catch blocks. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3648 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-27 03:59:10 +00:00
aaron 62bc7651a8 fix for PSPW with DbSNP mask. Added an integration test for this case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3628 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 19:31:32 +00:00
ebanks b6bceb39b0 Fixing up output for performance tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3619 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 17:00:17 +00:00
hanna 003dd4de3e Rev Picard with performance enhancements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 22:54:23 +00:00
ebanks b5df2705c9 -Remove Nway output option 
-Remove in-memory sorting
-Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag).

Cleaner, faster code.  Wiki has been updated (including how to use FixMateInformation.jar from Picard).  More changes coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 20:31:55 +00:00
ebanks 824c2bbac0 Finishing previous checkin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 17:21:38 +00:00
hanna c806ffba5f Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations 
will not be as fast as they could be because the workflow is currently merge sam records (sharding)
-> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split
records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext
is updated to take advantage of the new functionality in ReadBackedPileup.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3599 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-21 02:11:42 +00:00
depristo 57a13805da GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3596 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-19 21:36:41 +00:00
kiran 8ff93f77e6 Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3595 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 21:51:40 +00:00
rpoplin 724affc3cc Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 17:37:11 +00:00
aaron b978d5946b adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3584 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 08:23:23 +00:00
ebanks 01ffa307c2 When going NWay out in the cleaner, use the new *merged* header (instead of the original one) for each bam file so that it matches the new uniquified read group ids in the reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3569 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 19:36:36 +00:00
ebanks 7a91dbd490 Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 15:53:06 +00:00
ebanks 8c28be5933 Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this). 
Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 16:42:06 +00:00
ebanks ca4eab1d23 Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields. 
Added an integration test for the read-less case.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3525 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 20:36:46 +00:00
ebanks 9b2fcc4711 Refactoring of the annotation system: 
1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong.  Fixed the headers too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:05:51 +00:00
aaron 6d5556939d updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version 
to the vlidation directory), using the same md5sum.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 01:47:04 +00:00
depristo 6eeb1693ca JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 00:33:02 +00:00
depristo e2b41082af GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 22:26:32 +00:00