9dff578706
Added PG tag to bam header to let people know it's been cleaned.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
850f36aa61
Changes to the Unified Genotyper's arguments:
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1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:44:24 +00:00
cbed0b1ade
Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-29 22:50:17 +00:00
5dce16a8f1
Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 13:10:11 +00:00
7f4d5d9973
Ti/Tv by AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 17:56:29 +00:00
e7c0ded40e
Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:48:41 +00:00
f050beada6
make sure we do delete the temp file we create
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3244 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:32:49 +00:00
536f22f3bd
adding VC adaptor for GELI, along with unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 05:28:39 +00:00
e9e844fbf5
1. Reverting: dbsnp automatically is a comp
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2. Fixing logic for min Qscore calculation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:51:35 +00:00
532263ea25
Oooops, forgot to update the test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3229 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:38:24 +00:00
4abd3b0b7b
Fixing known/novel calc now that dbsnp isn't a default comp track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:43:59 +00:00
3b5673d967
1. Removed -all; by default all modules are used; use -none for no modules.
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2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 02:46:42 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
c44f63c846
Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3196 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 14:28:12 +00:00
abf48cee05
Moving over to VariantContext from Variation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3195 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 06:56:29 +00:00
d73c63a99a
Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.
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Also, adding some more useful integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 05:47:17 +00:00
be7cbf948b
adding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3186 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 17:41:48 +00:00
7adff5b81a
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:36:19 +00:00
e702bea99f
Moving VE2 to core; calling it "VariantEval" (one more checkin coming)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:25:47 +00:00
ac6f6363ce
Execs() temporarily disabled after removal of bam file. New tests forthcoming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3178 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:11:56 +00:00
ac9dc0b4b4
Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:53:02 +00:00
e413882302
Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 20:42:18 +00:00
d06c7835d8
Adding performance tests for the indel realigner; should take ~3 hours.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 04:45:22 +00:00
961ca05abc
Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 01:43:07 +00:00
fa01876255
UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 19:42:29 +00:00
71f38a9199
Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).
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Should take ~3 hours to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:30:59 +00:00
fba48b515a
Heads up everyone:
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For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:37:25 +00:00
7025f5b51d
Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 19:37:17 +00:00
9f6377f7fb
added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval.
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 15:37:15 +00:00
4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
f7d1b8f5de
CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.
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Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 16:27:23 +00:00
3d3d19a6a7
the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.
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a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 22:39:56 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
8ea98faf47
Deleting the pooled calcluation model -- no longer supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 11:44:27 +00:00
20e3ba15ca
Added an optional argument -rgbl --read_group_black_list to filter read groups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3079 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 19:38:57 +00:00
73a14a985b
Moving VariantsToVCF to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-26 18:55:12 +00:00
5079f35e40
better method names for read based reference ordered data access.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3069 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 16:13:31 +00:00
7462a0b2d1
cleaned-up of VariantContextAdapter tests, fixed the double comparisons in equals() in RodGeliText (nice MathUtils.compareDoubles Kiran)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3064 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 15:18:30 +00:00
a69b8555dd
Geli to variant context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3063 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 06:45:29 +00:00
eafdd047f7
GLF to variant context. Added some methods in GLF to aid testing; and added a test that reads GLF, converts to VC, writes GLF and reads back to compare.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3062 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 03:43:25 +00:00
ee1dc6092f
Test updated. Now we do not throw an exception when locus interval is out of bounds, we just return silently a reference context trimmed to the current shard boundaries. New test checks for trimming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3058 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 17:37:52 +00:00
4c4d048f14
Moving VariantFiltration over to use VariantContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3048 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 18:35:23 +00:00
c88a2a3027
Fixing/cleaning up the vcf merge util
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 15:13:32 +00:00
03480c955c
And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3039 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 04:58:37 +00:00
0311980668
The VariantAnnotator can now officially annotate genotype (FORMAT) fields.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 03:30:14 +00:00
0247548400
Fixed one test and (temporarily) punted on another
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3030 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 06:22:48 +00:00
ee0e833616
Some significant changes to the annotator:
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1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1 . Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 05:38:32 +00:00
2525ecaa43
Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3012 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 16:34:50 +00:00
6dd5f192e7
Performance improvements for RODs in conjunction with new sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3010 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-16 14:54:12 +00:00
ebanks
aaron
depristo
rpoplin
asivache
hanna
chartl
kshakir