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716 Commits (9d2a48553260fbd4e2d671266755140d1d98b6cd)

Author SHA1 Message Date
ebanks 9a05e8143d Move to 4.0 and away from VCFRecord. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3780 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 15:54:54 +00:00
ebanks 7e7da75d27 Moving over to 4.0 and away from VCFRecord 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3778 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 14:07:10 +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 e75b3e13bd updating unit test for previous fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3761 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 03:23:53 +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
aaron 3347d1ca7c part one of combining format and info header lines code into a single abstract class for Mark; plus some 'm' removals from access methods for Eric. Adding fixes for CombineVariants next. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3719 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 05:57:58 +00:00
weisburd 9ec393bfce Updated md5 - vcf header line change 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3714 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 21:02:09 +00:00
depristo 61e2b2e39b Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3710 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 13:32:33 +00:00
aaron 3093a20a55 fixing VCF header format and info fields so that they propery emit the unbounded count value correctly for vcf4 or vcf3. Eric we should update the vcf4 spec page to indicate format fields are allowed to use the unbounded count as well (if this is true). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3707 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 22:02:16 +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
aaron 43ca595d15 VCF headers now can be set to a particular VCF version after creation, which converts the header lines to the appropriate encoding on output. Plus some clean-up of the code. 
Also commented out the Tribble index out-of-date tests, the timing seems to be troublesome from the farm.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3702 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 05:32:14 +00:00
hanna 4995950d04 IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 04:40:31 +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
aaron 844cb2ed33 fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric! 
Also putting more tolerance into the timing on the tibble index tests (that check to make sure we're deleting out of date indexes, and not deleting perfectly good indexes).  It seems that some of the farm nodes aren't great with a stopwatch.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3674 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 21:38:55 +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
aaron 62d22ff1aa adding the original allele list to a variant context (as the annotation ORIGINAL_ALLELE_LIST), in the case where the set alleles are the result of clipping. Added tests for both cases. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3658 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 17:23:46 +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 09ccdf83b2 fixing a broken test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3647 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 21:59:00 +00:00
aaron 5f8a3f95ef The GT field once again reigns supreme (it must be the first genotype field). Thanks for the catch Eric. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3645 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 21:03:05 +00:00
aaron b3edb7dc08 two fixes for the VCF 4 parser: 
- Allow the "GT" field in genotypes at any point in the genotype string (before we required they be the first key-value pair).
- Fix a bug with the phasing value put into the VariantContext, thanks for the catch Guillermo!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3638 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 18:01:23 +00:00
weisburd e15fe6858e Disabling test - Will need to update big-tables soon.. will re-enable after updating md5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3637 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 15:43:41 +00:00
aaron 682f9b46c6 Two fixes together: 
1) Some improvements to the VCF4 parsing, including disabling validation.
2) Reimplemented RefSeq in the new Tribble-style rod system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3630 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 22:17:03 +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
aaron 8a9b2f4256 removing the GLF ROD. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3624 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 22:51:45 +00:00
aaron 611d834092 a couple of VCF 4 improvements: 
-Validation of INFO and FORMAT fields.
-Conversion to the the correct type for info fields (i.e. allele frequency is now stored as a float instead of a string).
-Checks for CNV style alternate allele encodings( i.e. <INS:ME:L1>), right now we exception out.  Maybe we should just warn the user?
-Tests for the multiple-base polymorphism allele case.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3622 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 20:21:43 +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
aaron 0cafd3d642 clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3614 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 22:42:38 +00:00
aaron 9872b65803 clip to the null allele on the reference string in VCF 4, instead of stopping to perserve one reference base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3613 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 20:52:19 +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
aaron a6d3e4bd47 Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes). 
This check-in will temperarly break the build (I need to see if Bamboo is correctly returning the log file for the failed builds).  

Will be fixed once Bamboo starts building.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3609 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 18:26:37 +00:00