d4e7655d14
Added ability to call multiallelic indels, if -multiallelic is included in UG arguments. Simple idea: we genotype all alleles with count >= minIndelCnt.
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To support this, refactored code that computes consensus alleles. To ease merging of mulitple alt alleles, we create a single vc for each alt alleles and then use VariantContextUtils.simpleMerge to carry out merging, which takes care of handling all corner conditions already. In order to use this, interface to GenotypeLikelihoodsCalculationModel changed to pass in a GenomeLocParser object (why are these objects to hard to handle??).
More testing is required and feature turned off my default.
2012-01-06 11:24:38 -05:00
dd80ffbbbe
Merged bug fix from Stable into Unstable
2012-01-05 21:51:48 -05:00
c96fee477c
Bug fix for VariantSummary
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-- Call sets with indels > 50 bp in length are tagged as CNVs in the tag (following the 1000 Genomes convention) and were unconditionally checking whether the CNV is already known, by looking at the known cnvs file, which is optional. Fixed. Has the annoying side effect that indels > 50bp in size are not counted as indels, and so are substrated from both the novel and known counts for indels. C'est la vie
-- Added integration test to check for this case, using Mauricio's most recent VCF file for NA12878 which has many large indels. Using this more recent and representative file probably a good idea for more future tests in VE and other tools. File is NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.vcf in Validation_Data
2012-01-05 21:51:06 -05:00
f5e10e9879
Merged bug fix from Stable into Unstable
2012-01-05 15:35:09 -05:00
18ed954741
Compute Ti/Tv only if bi-allelic
2012-01-05 15:33:26 -05:00
a6886a4cc0
Initial commit of the Active Region Traversal. Not ready to be used by anyone yet.
2012-01-04 17:03:21 -05:00
58d4539304
Enabled banded indel computation by default. Reversed logic in input UG argument so that we can still disable it if required. Minor changes to integration tests due to minor differences in GL's and in annotations
2012-01-04 15:28:26 -05:00
9ff8a01da2
Merged bug fix from Stable into Unstable
2012-01-03 18:10:39 -05:00
9b55505c03
Fixing PairHMMIndelErrorModel array out of bounds
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This error was due to the ReadClipper change of contract. Before the read utils would return null if a read was entirely clipped, now it returns an empty (safe) GATKSAMRecord.
2012-01-03 18:08:46 -05:00
2c3a9ce02f
Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
2012-01-03 17:25:56 -05:00
621ee2b613
Merged bug fix from Stable into Unstable
2012-01-03 16:56:49 -05:00
9093de1132
Cleanup: remove code to calculate the MLE AC in the UGE.
2012-01-03 15:58:51 -05:00
2d093828a4
Final changes to Junky (been frozen for a while, but uncommitted) and the qscript for it. A first cursory implementation of the trellis-based Exact AC-constrained genotyping algorithm in UGE. Nothing calls into it, so this should be entirely safe (and, no surprise, it passes UG integration tests).
2012-01-03 15:33:04 -05:00
ea6e718cb8
SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline.
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For now, we recommend only running with the GRCh37.64 database.
2012-01-03 15:18:36 -05:00
93e1417b6e
Update to the VSS GATK documentation.
2012-01-03 13:39:31 -05:00
393993e0c7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-31 20:42:46 -05:00
a259bfefd4
First commit addressing problems running RTC in parallel.
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Turns out that because the RTC is the first walker to 'correctly' tree reduce according to functional programming
standards, the RTC has revealed a few problems with the tree reducer holding on to too much data. This is the first
and smaller of two commits to reduce memory consumption. The second commit will likely be pushed after GATK1.4 is
released.
2011-12-29 16:22:14 -05:00
1a45ea5a05
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-29 11:37:15 -05:00
d20a25d681
A much better way of choosing the alternate allele(s) to genotype in the SNP model of UG: instead of looking at the sum of base qualities (which can and did lead to us over-genotyping esp. when allowing multiple alternate alleles), we look at the likelihoods themselves (free since we are already calculating likelihoods for all 10 genotypes). Now, even if the base quals exceed some arbitrary threshold, we only bother genotyping an alternate allele when there's a sample for which it is more likely than ref/ref (I can generate weird edge cases where this falls apart, but none that model truly variable sites that we actually want to call). This leads to a huge efficiency improvement esp. for exomes (and esp. for many samples) where we almost always were trying to genotype all 3 alternate alleles. Integration tests change only because ref calls have slight QUAL differences (because the best alt allele is still chosen arbitrarily, but differently).
2011-12-27 16:50:38 -05:00
adff40ff58
Minor optimizations to avoid extra processing (esp. for reduced reads)
2011-12-27 13:16:25 -05:00
17bfe48d5e
Made all class methods private in the ReadClipper
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* ReadClipperUnitTest now uses static methods
* Haplotype caller now uses static methods
* Exon Junction Genotyper now uses static methods
2011-12-27 02:11:32 -05:00
dd990061f6
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-26 14:45:35 -05:00
2130b39f33
Found the bug in the engine: RodLocusView was using the wrong seek method so that it would only move to the first locus of a shard (and with multi-locus shards, this meant that we never processed RODs from the other positions). In fact, because the seek(Shard) method is extremely misleading and now no longer used, I think it's safer to delete it and make everyone use the much more transparent seek(GenomeLoc). Note that I have not re-enabled my improvements to the intervals accumulation of ReferenceDataSource because that inefficiency is still present downstream in RodLocusView; need to discuss those changes with Matt.
2011-12-26 14:45:19 -05:00
506c0e9c97
Disabling SnpEff support in the GATK and SnpEff annotation in the HybridSelectionPipeline
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SnpEff support will remain disabled until SnpEff 2.0.4 has been officially released
and we've verified the quality of its annotations.
2011-12-23 19:12:57 -05:00
24c84da60d
'Fixing' the changes in ReferenceDataSource so that a shard properly contains a list of GenomeLocs instead of a single merged one. However, that uncovered a probable bug in the engine, so instead of letting this code fester unfixed in the build (affecting everyone in the group) I've decided to revert the previous (slow, but working) version and fix the engine in my own branch.
2011-12-23 15:39:12 -05:00
8762313a0d
Better TODO message
2011-12-22 20:54:35 -05:00
a815e875a8
Removing debugging output
2011-12-22 15:49:11 -05:00
deef542a38
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-22 15:44:58 -05:00
6d260ec6ae
Start printing traversal stats after 30 seconds. I can't stand waiting 2 minutes.
2011-12-22 15:40:59 -05:00
07128a2ad2
ReadUtils cleanup
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* Removed all clipping functionality from ReadUtils (it should all be done using the ReadClipper now)
* Cleaned up functionality that wasn't being used or had been superseded by other code (in an effort to reduce multiple unsupported implementations)
* Made all meaningful functions public and added better comments/explanation to the headers
2011-12-20 17:48:40 -05:00
f73ad1c2e2
Bugfix/Rewrite: Algorithm to determine adaptor boundaries
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The algorithm wasn't accounting for the case where the read is the reverse strand and the insert size is negative.
* Fixed and rewrote for more clarity (with Ryan, Mark and Eric).
* Restructured the code to handle GATKSAMRecords only
* Cleaned up the other structures and functions around it to minimize clutter and potential for error.
* Added unit tests for all 4 cases of adaptor boundaries.
2011-12-20 17:48:39 -05:00
7204fcc2c3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-20 12:59:11 -05:00
8ade2d6ac2
max_alternate_alleles also ready to be made public
2011-12-20 12:59:02 -05:00
6f52bd580b
--multiallelic mode is not hidden anymore (but it is annotated as advanced); added docs
2011-12-20 12:47:38 -05:00
24585062f8
Merge branch 'incoming'
2011-12-19 23:16:36 -05:00
67298f8a11
AFCR made public (for use in VSS)
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Minor changes to ValidationSiteSelector logic (SampleSelectors determine whether a site is valid for output, no actual subset context need be operated on beyond that determination). Implementation of GL-based site selection. Minor changes to EJG.
2011-12-19 23:14:26 -05:00
06d385e619
Simplifying the interface a bit
2011-12-19 15:29:46 -05:00
339ef92eac
Goodbye SW by default. Now aligned reads that overlap intron-exon junctions are scored where they are by default, but warns the user (and flags the record in the VCF) if there's evidence to suggest that there is an indel throwing off the scoring (e.g. if the best score of a realigned unmapped read is >5 log orders better than the best score of a scored mapped read). Unmapped reads are still SW-aligned to the junction-junction sequence. This should result in a rather massive speedup, so far untested.
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UGBoundAF has to go in at some point. In the process of rewriting the math for bounding the allele frequency (it was assuming uniform tails, which is silly since i derived the posterior distribution in closed form sometime back, just need to find it)
2011-12-19 12:18:18 -05:00
418d22b67e
Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IntronLossGenotyperV2.java
2011-12-19 10:59:18 -05:00
69661da37d
Moving ValidationSiteSelector to validation package in public under my ownership. JunctionGenotyper added and modified several times, this commit is due to merging conflix fixes.
2011-12-19 10:57:28 -05:00
16cc2b864e
- Corrected bug causing cases where both parents are HET to be accounted twice in the TDT calculation - Adapted TDT Integration test to corrected version of TDT
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Signed-off-by: Ryan Poplin <rpoplin@broadinstitute.org>
2011-12-19 10:30:59 -05:00
5fd19ae734
Commented exactly how the results are represented from the exact model so developers can know how to use them.
2011-12-19 10:19:00 -05:00
3069a689fe
Bug fix: if there are multiple records at a given position, it turns out that SelectVariants would drop all variants that follow after one that fails filters (instead of dropping just the failing one). Added an integration test to cover this case.
2011-12-19 10:04:33 -05:00
5b678e3b94
Remove ClippingOp UnitTests
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* all testing functionality is in the ReadClipperUnitTest, no need to double test.
* class and package naming cleanup
2011-12-19 07:49:26 -05:00
1ead00cac5
New fork of SamFileHeaderMerger should be cached at the thread level to enable fast (and valid) thread lookups.
2011-12-18 19:04:26 -05:00
bc842ab3a5
Adding option to VariantAnnotator to do strict allele matching when annotating with comp track concordance.
2011-12-18 15:27:23 -05:00
953998dcd0
Now that getSampleDB is public in the walker base class this override in VariantAnnotator isn't necessary.
2011-12-18 14:38:59 -05:00
07f9d14d9f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-12-18 00:43:15 -05:00
c5ffe0ab04
No reason to sum the normalized posteriors array to get Pr(AF>0) given that we can just compute 1.0 - array[0]. Integration tests change only because of trivial precision artifacts for reference calls using EMIT_ALL_SITES.
2011-12-18 00:31:47 -05:00
6dc52d42bf
Implemented the proper QUAL calculation for multi-allelic calls. Integration tests pass except for the ones making multi-allelic calls (duh) and one of the SLOD tests (which used to print 0 when one of the LODs was NaN but now we just don't print the SB annotation for that record).
2011-12-18 00:01:42 -05:00
Guillermo del Angel
Mark DePristo
Eric Banks
Ryan Poplin
Mauricio Carneiro
Christopher Hartl
David Roazen
Matt Hanna
Laurent Francioli