getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled). Probably we should change the method to be getNeg10Log10PError(). Anyone have strong feelings on this?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 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
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
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. 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
[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
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
This will output for hapmap variant sites:
chromosome position ref allele variant allele number of variant alleles of the individuals depth of coverage power to detect singletons at lod 3 number of variant bases seen whether or not variant was called
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 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
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. 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
depristo
chartl
ebanks
rpoplin
aaron
hanna