management code. Currently, will not work when neither -varout nor -vf are specified, but should work in all other
cases.
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This change allows the pooled calculation model to work correctly with multiple threads. Boys, the Genotyper is now officially parallelized.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2462 348d0f76-0448-11de-a6fe-93d51630548a
Pooled calling now takes less than half the time it used to.
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Also, array size for caches should be max score + 1.
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The major effects of this commit are as follows:
1. We no longer skip any good bases (of course, this change alone breaks every single integration test).
2. The dinuc covariate returns a "no dinuc" value for the first base of a read (but not for the last base anymore, since there is a valid dinuc) or if the previous base is a bad base (e.g. 'N').
I've done a bunch of testing on real data and everything looks right; however, let's wait until the recalibrator guru gets back from vacation next week and can double-check everything before shipping this out in another early access release.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2443 348d0f76-0448-11de-a6fe-93d51630548a
Still experimental. As of now, it's not useful. More analysis is needed to determine how to handle cases where UG is unsure whether a sample is het or hom.
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Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.
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1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.
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1: all overlapping and abutting intervals merged (ALL),
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY),
3: no merging (NONE). This option is not currently allowed, it will throw an exception. Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.
The command line option is --interval_merging or -im
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1. allele balance annotation is now weighted by genotype quality (so we don't get misled by borderline het calls)
2. Updates to the Unified Genotyper for parallelization:
a. verbose writing now works again; arg was moved from UAC to UG
b. UG checks for command that don't work with parallelization
c. some cleanup
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The cycle covariate is now first/second of pair aware. I'm taking it on faith from both Chris Hartl (waiting on slides from him) and Tim that this is the right thing to do. We'll have Ryan confirm it all next week.
The only change is that if a read is the second of a pair, we multiple the cycle by -1 (a simple way of separating its index from that of its mate).
Of course, this broke all integration tests.
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depending on its output format. Current implementation is probably a bit overkill-ish and
we can whittle this down to what's absolutely necessary.
Writing VCFs to the 'out' protected printstream may not work at this moment.
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Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.
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this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.
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Added - A paired read order covariate to use with recalibration. Currently experimental: for instance, what's a proper pair versus just a pair? Nobody should use this one...
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Adding first pass of stub and storage classes for the GenotypeWriters so that UG can be parallelizable. Not hooked up yet, so UG is unchanged.
The mergeInto() code in the storage class is ugly, but it's all Tribble's fault. We can clean it up later if this whole thing works.
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2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant())
3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it.
4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization.
5. Improved some of the UG integration tests.
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shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
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1. push the ReadBackedPileup filtering up into the ReadFilters for read-based filters
2. stop querying the cigar for its length (just do it once)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2381 348d0f76-0448-11de-a6fe-93d51630548a
Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.
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Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.
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Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).
Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.
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This is a temporary fix - pushed more elegant solution over to Matt.
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[Also, enable Mark's new UG arguments]
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1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
below the specific command-line arguments for the walker. Also introduced
@help.summary to override summary descriptions if required.
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Also increased the line width as much as I could tolerate (100 characters -> 120 characters).
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The only major difference is that we are now able to get accurate allele balance ratios.
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This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands.
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Convert it from a completely wonky solution to a slightly less wonky solution
that will work in more cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2310 348d0f76-0448-11de-a6fe-93d51630548a
- Hook up Variation and Genotype in SSG
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a
-Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H).
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- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit
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We are now VCF3.3 compliant.
(Only a few more stages left. Sigh.)
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feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
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VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype.
Because of this change, RodVCF is now just a wrapper around the VCFRecord and does nothing else. Also, one can call toVariation on the VCFGenotypeRecord and it returns the VCFRecord.
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This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers. I haven't finished refactoring the writers and haven't even touched the readers at all.
The major changes here are that
1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes
2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called).
The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a
and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
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in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
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-added code to cache the allele list so it didn't need to get recomputed each time it was requested.
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2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
I am now at a point where I can merge the functionality from other coverage walkers into this one.
Thanks to Andrew for input.
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- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a
- Moved validation walkers to new qc dir
- Killed unused test
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- Use QualityUtils when phred-scaling now
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- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable
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-Renamed methods to be more consistent.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
- Added implementation of -bySample in DoCWalker
- Removed CoverageBySample and added a watered down version to the examples directory
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Moved/killed a few other walkers (with permission).
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- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
- VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
- A PileupWalker integration test on a particularly nasty FHS site
- Two second-base annotation related integration tests on that same site
+ outputs were all hand-validated in matlab; within a certain tolerance for the annotations
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Finished converting genotyper and annotator code to new ReadBackedPileup system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2192 348d0f76-0448-11de-a6fe-93d51630548a
I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken.
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Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs).
Technically, VCF records can be indels now.
More changes coming
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1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having).
2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler)
UG now runs in half the time for JOINT_ESTIMATE model.
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[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]
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Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space.
Update to the integration test so bamboo doesn't look as though someone murdered it with a spork
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Added integration test for pooled model and updated other joint estimation tests to be more comprehensive now that they are faster.
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2. UG: don't print slod if lods are infinite (todo: figure out a good guess instead)
3. UG: if probF=0 for 2 alt alleles are both 0 (because of precision), use log values to discriminate
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2. Retired allele frequency range from UG, which wasn't very useful.
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- For all reference bases, the proportion of their second best bases that support the SNP
- the proportion of non-reference bases that support the SNP
and reports the difference between the two. Initially I was taking depth into account as well, but that did not appear to work as nicely as I'd like (even at 20,000x depth, if 95% of the non-reference bases are C, and 98% of the reference second-best-bases are C, then we would want to be suspicious of it; but perhaps slightly less so than if the depth were only 20...)
Anyway it's now available. I'm not sure how useful it will be, but I spawned the FHS annotation jobs again, so we'll see.
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[There was no reason to enforce that every VCF being output from the GATK should have the samples sorted, since someone might want them ordered non-alphabetically]
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Updated the integration tests that were failing to due to different ordering of genotyping entries in VCF, I'll check in the VCF diff tool I wrote when I get a cycle or two.
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-If qscore is infinity (because of precision) make a best guess instead
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2. Allele frequency spectrum is not emitted for single samples (since it doesn't make sense).
3. If in pooled mode, throw an exception of pool size isn't set appropriately.
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We totally *do* want to annotate the call if called by another walker. Totally boneheaded misenterpretation of what the code was doing -- Eric, please forgive me for being an idiot.
Instead, change the StingException to what it really should be -- an IllegalStateException, which is not coincidentally already handled by the calling function.
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do **not** attempt to annotate if UnifiedGenotyper is called from another walker! Why this didn't break the build earlier I have no idea.
Ultimately, there should be a better way of interfacing UG with another walker -- what if some other walker wants the annotations from UG? But since we're calling map directly -- and the annotations don't get returned directly from map -- this needs to be handled differently, while the map function should ultimately return the LOD score or quality under the GCM alone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2066 348d0f76-0448-11de-a6fe-93d51630548a
Second base skew annotations and integration tests. Nothing need be given except -A SecondBaseSkew; the statistic it annotates calls with is a chi-square statistic given by the deviation of the observed proportion of reference second-best-bases from the expected 1/3. Future additions may be to ask that the deviation be instead from a given transition table.
A big note for all users: All IllegalStateExceptions from the variation ROD (e.g. the RodGeliText) are dealt with SILENTLY. I understand this isn't optimal, but I'd rather simply not annotate a non-bi-allelic site than fail completely (there are quite a few such sites even on the regions over which the integration test has been written).
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-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points
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VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper. UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).
This is a fairly all-encompassing check in. It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout. All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.
Stage 2 of the process will happen later this week.
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2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week).
3. Added integration tests for joint estimation model
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a
2. Don't print verbose output from SLOD calculation (it's just a repeat of previous output).
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Just stomped on the existing md5s because that's what Eric told me to do.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
1. Add dbsnp RS ID to VCF output from genotyper; to do this I needed to fix the dbsnp rod which did not correctly return this value.
2. Remove AlleleBalanceBacked and instead generalize the arbitrary info fields backing VCFs (and potentially others) in preparation for refactoring VariantFiltration next week.
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Revert until we find out whether the cause is legit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
-Don't restrict info fields to 2-letter keys
[about to move these to core]
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-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
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
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
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
-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
-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
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
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1902 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
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.
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Chris, if this breaks an integration test, you get it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
@PoolUtils - split reads by indel/simple base
@BaseTransitionTable - complete refactoring, nicer now
@UnifiedArgumentCollection - added PoolSize as an argument
@UnifiedGenotyper - checks to ensure pooled sequencing uses the appropriate model
@GenotypeCalculationModel - instantiates with the new PoolSize argument
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1867 348d0f76-0448-11de-a6fe-93d51630548a
Also moved a buch of Lists over to Sets for consistancy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a
-Add another filter for read groups for Chris
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Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1831 348d0f76-0448-11de-a6fe-93d51630548a
We currently get identical lods and slods as MultiSampleCaller (except slods for ref calls, as I discussed with Jared) and are a bit faster in my few test cases. Single-sample mode still emulates SSG.
The remaining to do items:
1. more testing still needed
2. we currently only output lods/slods, but I need to emit actual calls
3. stubs are in place for Mark's proposed version of the EM calculation and now I need to add the actual code.
More check-ins coming soon...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1821 348d0f76-0448-11de-a6fe-93d51630548a
For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input. For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.
The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you. More on that in a separate email.
Other minor cleanups added too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
Also, with Picard's latest changes, we need to make sure we don't double-close the sam writer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1779 348d0f76-0448-11de-a6fe-93d51630548a
-Adding initial version of Multi-sample calculation model. This still needs much work: it needs to be cleaned up and finished. Right now, it (purposely) throws a RuntimeException after completing the EM loop.
Also:
-Fix logic in GenotypeLikelihoods.setPriors
-Add logger to the models for output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1764 348d0f76-0448-11de-a6fe-93d51630548a
Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
Some notes:
1. This design should be flexible enough to include pooled calling (for now) after discussions with Chris.
2. Using the unified caller with the SingleSampleCalculationModel emits the exact same output as SSG over all of chr20 for NA12878. Additionally, when we include the "max deletions allowed at a locus" argument (so we don't try to call SNPs at deletion sites), it removed 233 SNP calls in chr20 that were clearly indel artficts.
3. The MultiSampleEMCalculationModel is still a work in progress and will be checked in later this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1740 348d0f76-0448-11de-a6fe-93d51630548a
hanna
rpoplin
asivache
depristo
ebanks
andrewk
aaron
alecw
chartl
kiran