956b570c8e
V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2721 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 18:37:17 +00:00
f6bca7873c
V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 04:10:16 +00:00
3399ad9691
Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 17:19:37 +00:00
476d6f3076
RealignerTargetCreator is officially live
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 03:41:52 +00:00
47440bc029
- Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads.
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- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 21:56:33 +00:00
a1054efe8a
Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 18:47:40 +00:00
c231547204
Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 13:53:29 +00:00
d6b9b788a8
Renamed -- PlinkRodWithGenomeLoc --> PlinkRod
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Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:19:28 +00:00
ac983e7a0b
Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained.
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****** PLINK ROD IS NOW READY TO GO ********
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:13:05 +00:00
ae22d35212
PlinkRod now correctly parses binary files without indels; unit test added for this behavior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 17:34:06 +00:00
94dc09c865
PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files.
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Upcoming: Test that the instantiation is correct, do it for indel-containing files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 16:13:24 +00:00
01db93299c
PlinkRodWithGenomeLoc now properly handels indels.
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There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 07:34:52 +00:00
42fb85e7f3
PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 06:19:26 +00:00
2ea768d902
ant clean is your friend....fixed test code dependent on an interface change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:07:46 +00:00
c1e09efb23
- Fixed output for beagle header
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- Better description for QualByDepth annotation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:25:56 +00:00
5b2a1e483e
Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 17:35:20 +00:00
9c7b281b4f
Set default value for max_coverage to be 100K (since 10K is too small).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 20:15:25 +00:00
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:36:49 +00:00
a1b4cc4baf
changes to intelligently log overflowing locus pile-ups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 08:09:48 +00:00
4ac9eb7cb2
- Smarter strand bias calculation
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- Better debug/verbose printing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 03:01:26 +00:00
9e0ae993c7
-B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2632 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:33:13 +00:00
c98df0a862
Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:18:02 +00:00
12453fa163
Misc cleanup of UG args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 04:38:52 +00:00
d8e74c5795
Update to MD5s for old tests and added extensive VCF testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2615 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:22:58 +00:00
b911b7df82
Fixing the AC annotation to be in line with the VCF spec
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2593 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:28:52 +00:00
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:18:59 +00:00
df998041a8
Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 16:31:25 +00:00
b19bb19f3d
First successful test of new sharding system prototype. Can traverse over reads from a single
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BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 03:35:55 +00:00
db9570ae29
Looks bigger than it is:
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* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 00:14:35 +00:00
cff8b705c0
Oh, and the test would not work anymore...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2585 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 17:47:09 +00:00
9bf0d7250a
Fixing the testOtherOutput UG integration test so it will run.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2580 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 13:40:14 +00:00
424d1b57f7
Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2577 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 23:22:37 +00:00
f96b2b211e
My last checkin updating R code broke an unrelated UnifiedGenotyper integration test. Eric says that I should take out the verbose test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2576 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 22:28:10 +00:00
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 20:09:10 +00:00
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).
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SequenomToVCF now correctly has no-calls when probes fail.
Re-enabled SequenomToVCF integration test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2572 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 15:40:27 +00:00
6d1107a4ed
Update to SequenomToVCF
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Output changing slightly so integration test disabled temporarily
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2571 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 15:32:05 +00:00
f99586f91b
Added integration test for beagle and verbose output in UG.
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Minor cleanup of VCFRecord code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 03:55:24 +00:00
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:50:39 +00:00
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).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:47:43 +00:00
03b7d5f5c7
1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation.
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2. Made RankSumTest abstract; added 2 subclasses: BaseQualityRST and MappingQualityRST (the latter based on a suggestion from Mark Daly). Untested so they're still experimental.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2561 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:33:53 +00:00
040fdfee61
Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter.
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I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2558 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 21:42:12 +00:00
42aff1d2c3
Annotator in general should be able to annotate monomorphic or tri-allelic sites.
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It's up to the individual annotations to decide whether they want to annotate or not.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 19:52:18 +00:00
dfa3c3b875
Added:
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SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft,
but is working as expected on a test ped file, which is included as an integration test.
Modified:
VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call
Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used
(caused me all kinds of confusion when I was basing SequenomToVCF off of it)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 17:17:21 +00:00
62dd2fa5be
Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2553 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 14:28:52 +00:00
9cbae53ee1
Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2548 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 15:19:22 +00:00
dfcd5ce25b
Fixed broken test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2547 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 06:13:01 +00:00
d5ab002449
Curiously, it seems I never set the default base quality used by the Genotyper to 10. It's done now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2546 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 06:02:01 +00:00
b468369dfa
-UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one)
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-MQ0 annotation is now standard again
-Added AC and AN annotations to VCF output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2545 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-08 05:40:42 +00:00
f587ff46af
Tile is now a standard covariate. By default the TileCovariate returns -1 if tile can't be derived from the read's name. Added a new command line option -throwTileException which will force TileCovariate to throw an exception if tile can't be derived for a read. Singleton covariates, such as any read group without tile info, must be skipped over in TableRecalibration so that the sequential formulation doesn't apply the same correction more than once. TileCovariate class has been added to the Early Access package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2544 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 22:51:41 +00:00
5f58492401
A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 21:17:39 +00:00
depristo
ebanks
rpoplin
chartl
aaron
hanna
asivache