d534241f35
Major revamp of annotations for indels:
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a) All rank sum tests now work for indels including multiallelic sites. For the latter cases, rank sum test is REF vs most common allele
b) Redid computation of HaplotypeScore for indels. It's now trivially easy to do because we are already computing likelihoods of each read vs haplotypes in GL computation so we reuse that if available. For multiallelic case, we score against N haplotypes where N is total called alleles.
Drawback is that all cases need information contained in likelihood table that stores likelihood for each pileup element, for each allele. If this table is not available we dont annotate, so we can only fully annotate indels right now when running UG but not when running VariantAnnotator alone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5947 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 15:34:24 +00:00
53667ce8fa
Disabled test that checks whether output is the same whether in Genotype Given Alleles mode or not - it won't as long as extended events are finally removed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5945 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 00:52:54 +00:00
35df80de14
Updated md5 due to changes to changes in QUAL field when in Genotype given alleles mode w/indels when in insertions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5944 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 23:52:38 +00:00
b93829e505
The underlying bam file for this test was busted for many reasons preventing Picard folks from making unrelated changes, so I needed to fix it. Updating md5s accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5943 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 22:26:06 +00:00
420d8feff6
No one should be calling the createHeader method(s) directly, but instead should be going through the full readHeader method (because it first sets the version); therefore I made them package protected and merged them. Updated the various unit tests that were using createHeader and were dangerously assuming that the header version was defaulting to 4.0 (which it no longer does).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5934 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 02:17:37 +00:00
dd6d61c031
Adding integration test to cover the case of a read that only covers an insertion (i.e. no M in the CIGAR string).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5923 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 21:02:47 +00:00
092952db44
After verifying that the changes to these tests were all in the RankSum annotations, I'm commiting fixes to the test md5s.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5918 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 13:01:18 +00:00
2b5683909e
Updated VQSR integration tests because of the new Omni file. Fixed overflow condition in FisherStrand when the depth is too high.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5910 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-01 14:20:37 +00:00
44cb7e4980
Renaming to make grepping through the output less confusing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5908 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-31 19:54:44 +00:00
9e834391fe
We now skip over all covering RODs in the BQSR as intended instead of just those which can be converted into a VariantContext. All the integration tests change because of subtleties in how certain dbsnp rod records are being converted into VCs. Added integration test which uses a bed file as the list of known polymorphic sites.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5892 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 16:32:17 +00:00
8ed82e5a08
The previous version of the UG was always creating BAQ'd pileups for the underlying site QUAL calculation. This resulted in some slowdown in the code. But as far as I can tell, the code actually didn't apply the BAQ'd base quality anywhere when the BAQ field wasn't in the read, so this just saves us 20% of the runtime when BAQ isn't enabled from heading into the BAQ subsystem when we don't actually want to get the BAQ'd base qualities.
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Fixed minor problem with WalkerTest for "" (for parameterization) md5s.
Added an explicit integrationtest for BAQ NONE
Now only creates the BAQ'd pileup, if the useBAQPileup parameter is provide in initializeAlternateAllele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5891 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 14:00:52 +00:00
f7298f4a7f
First of many baby steps to redo way in which we trigger events for indel calling and to eliminate extended events: get rid of SpanningDeletions annotation for indels. It's completely useless, and even more so once we no longer trigger at extended events (because we'll trigger by definition a base before a deletion starts, so deletions present in the current pileup are not informative).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5876 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 00:49:23 +00:00
e582a92af6
WalkerTest now checks for valid md5s in the integrationtests themselves, so no more stray whitespace errors. Added a WalkerTestTest to ensure tha t bad MD5s are detected and an error thrown
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5865 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 14:34:55 +00:00
06486c134a
Kill extra space in the md5.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5863 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 12:00:31 +00:00
cf3dbfee97
Renamed variantMergeOptions to filteredRecordsMergeType, as this is really what it does. Cleaned up the wiki so that it's clear what this does, as well as included an example of how to create an intersection with CombineVariants and SelectVariants. Added integrationtests of CombineVariants with OMNI and HapMap that deal with the two ways to merge fitlered/unfiltered records at the same site.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5860 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 01:54:29 +00:00
4bfec4c55b
Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5856 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:32:53 +00:00
480859db50
Contractified version of MannWhitneyU. Some behavior has been changed:
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- Running a test when there are no observations of at least one of the sets now breaks the MWU contract
+ MWU returns Pair(Double.NaN,Double.NaN) in these instances to maintain the contract of never returning null
+ No more Double.Infinity values will appear
- RankSumTests now probe the return values for NaNs, and don't annotate if they appear
- For small sets where the probability is calculated recursively, the z-value is now the inversion of the error function
and not the approximate z-value
- UG and Annotator integration tests updated to reflect changes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5845 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 13:57:15 +00:00
6a49e8df34
Significant change to the way subsetting by sample works with monomorphic sites. Now keeps the alt allele, even if a record is AC=0 after the subset. Previously, the system dropped the alt allele, which I don't think is the right behavior. If you really want a VCF without monomorphic sites, use the option to drop monomorphic sites after subsetting. See detailed information below.
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Right now, if you select a multi-sample VCF file down (or one with filters I see) down to a smaller set of samples, and the site isn't polymorphic in that subgroup, then the alt allele is lost. For example, when selecting down NA12878 from the OMNI, I previously received the following VCF:
1 82154 rs4477212 A . . PASS AC=0;AF=0.00;AN=2;CR=100.0;DP=0;GentrainScore=0.7826;HW=1.0 GT:GC 0/0:0.7205
1 534247 SNP1-524110 C . . PASS AC=0;AF=0.00;AN=2;CR=99.93414;DP=0;GentrainScore=0.7423;HW=1.0 GT:GC 0/0:0.6491
1 565286 SNP1-555149 C T . PASS AC=2;AF=1.00;AN=2;CR=98.8266;DP=0;GentrainScore=0.7029;HW=1.0 GT:GC 1/1:0.3471
1 569624 SNP1-559487 T C . PASS AC=2;AF=1.00;AN=2;CR=97.8022;DP=0;GentrainScore=0.8070;HW=1.0 GT:GC 1/1:0.3942
Where the first two records lost the ALT allele, because NA12878 is hom-ref at this site. My change results in a VCF that looks like:
1 82154 rs4477212 A G . PASS AC=0;AF=0.00;AN=2;CR=100.0;DP=0;GentrainScore=0.7826;HW=1.0 GT:GC 0/0:0.7205
1 534247 SNP1-524110 C T . PASS AC=0;AF=0.00;AN=2;CR=99.93414;DP=0;GentrainScore=0.7423;HW=1.0 GT:GC 0/0:0.6491
1 565286 SNP1-555149 C T . PASS AC=2;AF=1.00;AN=2;CR=98.8266;DP=0;GentrainScore=0.7029;HW=1.0 GT:GC 1/1:0.3471
1 569624 SNP1-559487 T C . PASS AC=2;AF=1.00;AN=2;CR=97.8022;DP=0;GentrainScore=0.8070;HW=1.0 GT:GC 1/1:0.3942
The genotype remains unchanged, but the ALT allele is now preserved. I think this is the correct behavior, as reducing samples down shouldn't change the character of the site, only the AC in the subpopulation. This is related to the tricky issue of isPolymorphic() vs. isVariant().
isVariant => is there an ALT allele?
isPolymorphic => is some sample non-ref in the samples?
In part this is complicated as the semantics of sites-only VCFs, where ALT = . is used to mean not-polymorphic. Unfortunately, I just don't think there's a consistent convention right now, but it might be worth at some point to adopt a single approach to handling this. Wiki docs updated.
Does anyone have critical infrastructure that depends on the previous convention? Let me know so we can coordinate the change.
There's a new function subContextFromGenotypes() that also takes a Set<Allele> to handle this type of behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5832 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-21 13:59:16 +00:00
e16bc2cbd9
Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this.
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Refactored several Interval utilties from GenomeLocParser to IntervalUtils, as one might expect they go
Removed GenomeLoc.clone() method, as this was not correctly implemented, and actually unnecessary, as GenomeLocs are immutable. Several iterator classes have changed to remove their use of clone()
Removed misc. unnecessary imports
Disabled, temporarily, the validating pileup integration test, as it uses reads mapped to an different reference sequence for ecoli, and this now does not satisfy the contracts for GenomeLoc
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5827 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-20 15:43:27 +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
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
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
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
3882d1b9c0
fixing the build \o/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5767 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-05 00:57:49 +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
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
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
deed7c47a1
Continuing the epic fail, some of our existing integration tests were wrong because of the lazy loading failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5712 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 17:54:41 +00:00
ab9ffb1a74
Epic failure on the lazy loading of genotypes: if the input VCF had its samples unsorted and we used a walker that didn't require genotypes, then we would sort the samples but not load genotypes (and therefore the genotypes wouldn't match the samples anymore). Added simple integration test to cover this case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5711 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-29 16:03:45 +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
45081c32d7
continuing from last night, the integration tests weren't covering the right behavior either
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5706 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-28 13:30:57 +00:00
600617a63c
Enabled code to deal with hard-clipping adaptor sequence when processing reads in pileup in indel caller. Proven now that changes are minimal (4 less calls in NA12878 chr20, quals slightly different), minor changes in vcf fields in integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5679 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-22 14:10:33 +00:00
49ea07acce
My fixes to Tribble yesterday revealed that some of the test VCFs for integration tests were actually malformed. Also, Guillermo updated the b37 dbSNP VCF and that broke some tests. Should be good for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5655 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-17 03:39:11 +00:00
8ed9c0f518
VariantsToTable now blows up by default if you ask for a field that isn't present in a record.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5636 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-14 14:42:43 +00:00
30a19a00fe
Fix for when running with EMIT_ALL_SITES but not GENOTYPE_GIVEN_ALLELES. Still want to emit a site even when over the deletion fraction for example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5617 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 20:07:06 +00:00
3b424fd74d
Enable new indel likelihood model by default, cleanup code, remove dead arguments, still more cleanups to follow. This isn't final version but at least it performs better in all cases than previous Dindel-based version, so no reason to keep old one around.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5615 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-12 17:54:46 +00:00
b6e7b5dace
Updating to reflect my recent Tribble fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5601 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 11:48:00 +00:00
cd61ef7169
Re-enabling multi-threaded integration tests. To make this work, downsampling and annotations are disabled for this test so that we don't have randomization issues for it based on which shards get executed first.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5597 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-08 03:07:39 +00:00
af09170167
As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5589 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-07 17:03:48 +00:00
3f3f35dea0
UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5585 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-06 19:06:24 +00:00
4b451314b2
Only store a read in the mate hash if it could possibly be moved. This reduces memory consumption especially when dealing with a case of tons of unmapped reads at the end of the bam; however, it's only mildly helpful for chr1 of the Papuans (there's a truly massive pileup 120Mb into it; more thought needed at a later point). Integration tests changed only because some of the reads in the original bam were busted to begin with (it's an old pilot 1000G bam).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5580 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-05 22:20:09 +00:00
095125152b
Updated to now longer include 2nd-best base output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5567 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-03 20:13:10 +00:00
3bcd4c5d75
--simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5521 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-26 14:57:18 +00:00
69646ff840
... and the corresponding integration test update
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2011-03-23 01:58:07 +00:00
1c95208e26
Finally found the bug that everyone is reporting on GS. Iterators on PriorityQueues aren't guaranteed to return elements in sorted order (a pretty stupid contract) - so we were passing items to the constrained writer out of order. Just do a Collections.sort instead (1 line of code). Happy father's day!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5476 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 21:28:19 +00:00
3e3ec85807
Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5433 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-13 15:24:22 +00:00
ee8f2871f7
A better output for Genotype Concordance summary. Now does only % comp hom-ref called hom-ref, het called het, and hom-var called hom-var, which are the quantities we typically show in slides. Updated intergration tests to reflect this change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5429 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 02:03:48 +00:00
3596c56602
New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so.
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2011-03-10 02:48:29 +00:00
ff7edc4493
Minor bug fix in empiricalMu prior calculation in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5412 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-10 00:42:38 +00:00
509daac9f7
Minor bug fix in k-means implementation. Updating VQSR integration tests in preparation for VQSRv2 by removing some unused features such as VariantDatum.weight and ti/tv cutting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5410 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-09 00:26:28 +00:00
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