-Improvement to snp genotype concordance test
And with that, it looks like I get revision #2000.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
Procedure:
1. Sites that are likely homozygous-variant but are called as heterozygous are identified.
2. For each site and read group, we compute the proportion of bases in the pileup supporting an alternate allele.
3. A one-sample, left-tailed t-test is performed with the null hypothesis being that the alternate allele distribution has a mean of 0.95 and the alternate hypothesis being that the true mean is statistically significantly less than expected (pValue < 1e-9).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1989 348d0f76-0448-11de-a6fe-93d51630548a
alignment start will confuse the sharding system and cause it to return duplicate reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality). Also, they now use ConcordanceTruthTable to keep track of necessary info.
GenotypeConcordance passes integration tests.
PooledConcordance needs to be finished by Chris.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a
It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1). Updated and checked BamToFastqIntegrationTest MD5 sums.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
ref genome. Make sure the reference genome is cached.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
-Make rods return the appropriate type of Genotype calls from getGenotype().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
One can now split up any number of sets into an N-way Venn (although it doesn't check for discordance in the calls, so you'll still want to use SimpleVenn for 2-way comparisons).
Wiki docs are updated.
To do: update to use Ryan's generic hash map when it's ready for public use.
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-Do the right thing in all models for all-base-mode (for Kiran).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1940 348d0f76-0448-11de-a6fe-93d51630548a
CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in.
Thanks to Kiran this was pretty easy...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a
the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
-VCF writer should be blind to the score/confidence/lod value - just print the thing out as is
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Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!).
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BTTJ - remove 'N's from previous base analysis -- even if both read and ref are 'N' (which does happen, occasionally)
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relationship between these two classes needs to be rethought; see JIRA
GSA-207.
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The whole GenotypeCall framework needs to be changed, but this will work for the time being.
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Integration test comment changed to reflect actual date of last md5 update.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
-Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1899 348d0f76-0448-11de-a6fe-93d51630548a
-Allow walkers calling the UG to pass in their own argument collections
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1896 348d0f76-0448-11de-a6fe-93d51630548a
VariantEvalWalker - whoops, wrote PooledGenotypeAnalysis rather than PooledAnalysis, now passes tests again
- PooledFrequencyAnalysis - don't bother initializing matrices if this isn't a pool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1895 348d0f76-0448-11de-a6fe-93d51630548a
+ Changes to doc
@ BasicPoolVariantAnalysis
+ use char rather than ReferenceContext
+ calculate # alleles
@ PooledFrequencyAnalysis
+ breakdown of call metrics by estimated number of alleles in pool
@ VariantEvalWalker
+ add PooledFrequencyAnalysis to analysis set
@ PooledGenotypeConcordance
+ correctly calculate maximal allele frequency for output
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Because it doesn't actually use EM, it's no longer a subclass of the EM model.
Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger). I need to deal with general UG output tomorrow. Hold off until then, Mark, and then you can go wild.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1891 348d0f76-0448-11de-a6fe-93d51630548a
Changed BaseTransitionTable to comparable objects for consistent ordering of output
( e.g. so the integration test doesn't yell so much )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1889 348d0f76-0448-11de-a6fe-93d51630548a
@ Pooled utils & power
- Removed two of the power walkers leaving only PowerBelowFrequency, added some additional
flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had
- Removed a number of PoolUtils variables and methods that were used in those walkers or simply
not used
- Removed AnalyzePowerWalker (un-necessary)
- Changed the location of Quad/Squad/ReadOffsetQuad into poolseq
@NQS
- Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType
@ BaseTransitionTable
- Added a slew of new integration tests for different flaggable and integral parameters
- (Scala) just a System.out that was added and commented out (no actual code change)
- (Java) changed a < to <= and a boolean formula
Chris
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a
ebanks
kiran
hanna
rpoplin
depristo
jmaguire
aaron
asivache
chartl
sjia