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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1942 348d0f76-0448-11de-a6fe-93d51630548a
-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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1932 348d0f76-0448-11de-a6fe-93d51630548a
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!).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a
kiran
hanna
rpoplin
depristo
ebanks
jmaguire
aaron
asivache
chartl