fe4b40ac2c
Adding new InbreedingCoeff and PercentNBases annotations for Guillermo to use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5823 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-19 19:50:39 +00:00
bc98ac1e74
Adding a TODO for future consideration
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5821 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-19 15:02:23 +00:00
0bb6b9a91a
Locus iterators were implemented in a peekable style, which meant that a locus
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and its three or four nearest neighbors could be in memory at once. Tweaking
the iterators to ensure that previous AlignmentContexts don't have strong
references which means that the garbage collector can work effectively to
help us trundle through these regions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5820 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 21:40:40 +00:00
a38b2be329
Fix for old, broken invariant where unmapped reads are represented by null rather than an empty BAMFileSpan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5819 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 20:57:38 +00:00
ebcd333ed8
Quick small updates:
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SelectVariants: typo
MethodsDevelopmentPipeline: Added CEU Trio WGS dataset
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5818 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 20:08:39 +00:00
4b00fd2688
Adding User Exception to VQSR for the case of trying to cluster with an annotation that doesn't exist in the input VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5816 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-18 19:47:51 +00:00
d698c87bbf
More UserExceptions and warnings in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5813 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 19:03:21 +00:00
a27e8b1dc6
Bug fix - use correct variable to retrieve from map.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5811 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 15:32:58 +00:00
d925f76edc
Cutting down on the number of info lines in VQSR so that I can read the warning messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5810 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-16 13:35:51 +00:00
5a7444e186
First step in refactoring UG way of storing indel likelihoods - main motive is that rank sum annotations require per-read quality or likelihood information, and even the question "what allele of a variant is present in a read" which is trivial for SNPs may not be that straightforward for indels.
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This step just changes storage of likelihoods so now we have, instead of an internal matrix, a class member which stores, as a hash table, a mapping from pileup element to an (allele, likelihood) pair. There's no functional change aside from internal data storage.
As a bonus, we get for free a 2-3x improvement in speed in calling because redundant likelihood computations are removed.
Next step will hook this up to, and redefine annotation engine interaction with UG for indel case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5809 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-15 23:04:11 +00:00
75db4705ab
Added splitContextByReadGroup() and fixed bug in getPileupForReadGroup() that resulted in a NPE when no reads where present for a read group.
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Added doc string for getNBoundRodTracks()
Intermediate commit for CalibrateGenotypeLikelihoods and GenotypeConcordanceTable, so I have a record of my work. Not ready for public consumption. Really looking forward to making local commits so I can track my progress without needing to push incomplete functionality up to the server.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5807 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-15 17:36:07 +00:00
fa75efb6ac
Backing off - need to change pileup interface for rank sum tests before indels can be annotated with them
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5804 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 21:54:54 +00:00
befbcd274b
Computes additional stats we want to use later for filtering: median and mad for indel position with respect to starts and ends of all the reads that support it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5803 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 21:19:58 +00:00
d4ca8d94fa
Trivial change to allow indels to be annotated by rank rum tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5801 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-13 20:24:08 +00:00
03452c15c0
Cleanup GATKBAMIndex unit test to allow a more efficient access pattern for
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FindLargeShards. Runtime of FindLargeShards on papuan dataset is now 75min.
GATK proper should benefit as well, although the benefits might be so small
as to not be measurable.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5798 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 21:50:33 +00:00
db1f9af679
Now supports multiple records in allele at sites that genotype as reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5796 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 17:36:27 +00:00
a22e98a2c4
Yikes. Fixing the build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5794 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 01:52:35 +00:00
40797f9d45
Ensuring a minimum number of variants when clustering with bad variants. Better error message when Matrix library fails to calculate inverse.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5793 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-12 01:48:37 +00:00
fb1be2653c
A succint walker that reports GC content by interval. Taking down two old implementations of the same thing from oneoffs. Documentation added to the wiki.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5790 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-11 18:53:11 +00:00
9a1d0d7076
Simple bug fix to allow multiple records at same site when genotyping given alleles. Takes only the first record (respecting filters, SNP type, etc), and issues a warning if there is more than one valid record at a site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5789 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-11 14:17:14 +00:00
dfdef2d29b
PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5787 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-11 12:07:44 +00:00
852e555c00
Fix broken functionality from previous commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5786 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 18:38:25 +00:00
8d47d2e813
Fix for Tim. It was possible for the constrained mate fixer to dump its cache in them middle of a given realignment (so the IndelRealigner was playing by the rules). No longer possible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5785 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 16:48:24 +00:00
3c364279f4
Add simple ability to create "X out of N" combined files: if a site is present in at least X input rods, it gets output, otherwise it's skipped, controlled with argument -minN.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5783 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 15:27:18 +00:00
f275be6968
A 'fat shard' finder. Cranks through the indices of a BAM file or list of
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BAM files looking for outliers (outliers right now are defined naively as
shards whose sizes are more than 5 stddevs away from the mean). Runs in
13 minutes per chromosome on 707 low pass whole genome BAMs -- not great, but
much faster than running UG on the same region to discover anomalies.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5782 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-10 12:56:47 +00:00
bf40351094
Minor update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5778 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-08 03:48:37 +00:00
15c7bd82a5
Fix for IndelRealigner memory problem. Now the Constrained mate fixing writer is told whether a read has been modified and, if it wasn't, can dump it when the cache needs to get flushed at places with tons of coverage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5777 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-06 19:34:41 +00:00
d8a761bbbd
Warn the user if trying to train with too few variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5776 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-06 17:47:58 +00:00
c2e8c460cb
Factor out all testing dependencies into a separate test configuration and
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only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5775 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 22:42:11 +00:00
b94d8dae17
Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5773 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 20:24:06 +00:00
7d7ce6cf00
Two embarassing bug fixes:
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a) Forgot to convert from phred to log-prob when computing gap penalties from recal table.
b) Forgot to uncomment code to correctly deal with hard-clipped bases in a read. But because of this, had to do a short term workaround to at least temporarily return class from hardClipAdaptorSequence to GATKSAMRecord. Otherwise, I get exceptions when casting because somehow some reads in HiSeq get to be SAMRecord (which GATKSAMRecord inherits from) but some reads get to be BAMRecords (which can't be cast into GATKSAMRecord), not sure why.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5771 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 17:08:34 +00:00
5c6965575e
Some refactoring that Mauricio and I worked through together. Changed filters
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to extend from org.broadinstitute.sting.gatk.filters.ReadFilter rather than
directly from net.sf.picard.filter.SamRecordFilter, which allows us to add
an initialize(GATKEngine) method so that filters can do any initialization
they'd like based on CL arguments, SAM headers, etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5760 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 19:29:08 +00:00
7ed8b4ddb0
Making sure CalculateLikelihoodsAndGenotypes returns an empty variant context when 'EMIT_ALL_SITES' and 'GENOTYPE_GIVEN_ALLELES' are being used, now for indels too!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5756 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 18:04:56 +00:00
6c7a0adc76
Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5750 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-04 13:56:01 +00:00
a19389528d
Bring back from the dead the old likelihoods model for indels, which has worse performance but is about 4x faster. Enabled with argument -GSA_PRODUCTION_ONLY in UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5748 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 22:38:33 +00:00
e5cc0f4eec
Added 'specificity' to variant eval's Validation Report evaluator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5742 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:48:30 +00:00
b88dec387c
clean up from VQSR movement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5741 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:35:30 +00:00
23cd3a7a5d
Moving VQSR v2 to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5740 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:20:06 +00:00
44a717f63a
Good bye VQSR v1. This commit will break the build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5739 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 20:09:52 +00:00
d4cbd8691c
Make the default that we only output SNPs (so that when I make another release we don't get flooded with questions about why the UG is all of a sudden so slow)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5729 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 16:38:55 +00:00
70f8ab6f89
Adding AF bin stratification for VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5728 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 15:22:50 +00:00
870e65a685
Fixing a build failure because I want to be completely sure that the code I
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checked in immediately following the build breaking code passes integration
tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5727 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-03 02:09:53 +00:00
411980a50a
Performance enhancements in GATKBAMIndex. Not sure these will assist in a
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normal use case, but they cut startup times and memory allocation noise in
the profiler, making my profiling time more productive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5726 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:48:16 +00:00
2a80ffa2ee
Totally experimental, barely useable not to be used yet implementation of an "Indel Quality Recalibrator" Idea is that any indel that's not in input dbsnp is treated as an artifact, and then a csv is built with # of indels and # of observations as a function of each input covariate (initially, only cycle, read group and homopolymer run are useful). Then, when computing likelihoods of indels based on input haplotypes we compute gap penalties based on value of covariates at read. Feature is disabled by default with hidden arguments. TBD if usefulness of feature is worth the extra time and pain.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5724 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 20:31:43 +00:00
fcf8cff64a
We didn't actually support all of these extensions. Updated to be accurate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5722 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-02 19:03:46 +00:00
34092fd32f
minor update...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5716 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 21:29:01 +00:00
36ac8beee1
Making the GATK unpredictably random...
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through an option!
set -ndrs if you want the GATK to be really random (non-deterministic). Engine option, available to every walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5715 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 19:29:08 +00:00
a5b96e0e04
I have to remember that this is Java, not C.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5709 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 17:40:14 +00:00
b7334dcc1e
Rank sum test annotations are the Z-scores from the test instead of the p-value.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5707 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 14:35:00 +00:00
f34e6d5b8c
Somewhere along the way someone broke this tool and failed to update the documentation to boot. Fixing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5705 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 03:16:20 +00:00
rpoplin
ebanks
hanna
carneiro
delangel
depristo
asivache