-Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2290 348d0f76-0448-11de-a6fe-93d51630548a
- 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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
We are now VCF3.3 compliant.
(Only a few more stages left. Sigh.)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2287 348d0f76-0448-11de-a6fe-93d51630548a
feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2271 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2267 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
-added code to cache the allele list so it didn't need to get recomputed each time it was requested.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2239 348d0f76-0448-11de-a6fe-93d51630548a
- 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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
- Use QualityUtils when phred-scaling now
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2217 348d0f76-0448-11de-a6fe-93d51630548a
- 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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
-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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
Moved/killed a few other walkers (with permission).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a
- 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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs).
Technically, VCF records can be indels now.
More changes coming
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2150 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a
[As a courtesy I fixed all instances once I was updating GenotypeLikelihoods]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a
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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a
Added integration test for pooled model and updated other joint estimation tests to be more comprehensive now that they are faster.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2123 348d0f76-0448-11de-a6fe-93d51630548a
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
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2116 348d0f76-0448-11de-a6fe-93d51630548a
2. Retired allele frequency range from UG, which wasn't very useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2113 348d0f76-0448-11de-a6fe-93d51630548a
- 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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2109 348d0f76-0448-11de-a6fe-93d51630548a
[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]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2092 348d0f76-0448-11de-a6fe-93d51630548a
-If qscore is infinity (because of precision) make a best guess instead
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2076 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2072 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2067 348d0f76-0448-11de-a6fe-93d51630548a
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).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2064 348d0f76-0448-11de-a6fe-93d51630548a
-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
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).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2032 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2028 348d0f76-0448-11de-a6fe-93d51630548a
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]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
-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
hanna
ebanks
rpoplin
depristo
chartl
alecw
aaron
asivache
kiran