Quals coming soon (four-base)
QHAT : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes.
Single Sample Calling:
Allele Frequency Metrics (LOD >= 5)
-------------------------------------------------
Total loci : 171575
Total called with confidence : 168615 (98.27%)
Number of variants : 111 (0.07%) (1/1519)
Fraction of variant sites in dbSNP : 87.39%
-------------------------------------------------
Hapmap metrics are coming up all zero. Will fix.
Pooled Calling:
AAF r-squared after EM is 0.99.
AAF r-squared after EM for alleles < 20% (in pools of ~100-200 chromosomes) is 0.95 (0.75 before EM)
Still not using fractional genotype counts in EM. That should improve r-squared for low frequency alleles.
Chores still outstanding:
- make a real pooled caller walker (as opposed to my experiment framework).
- add fractional genotype counts to EM cycle.
- add pool metrics to the metrics class? *shrug* we don't really have truth outside of a contrived experiment...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@380 348d0f76-0448-11de-a6fe-93d51630548a
* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
to make sure not to have an ArrayIndexOutOfBoundsException thrown.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@297 348d0f76-0448-11de-a6fe-93d51630548a
- Corrected some bugs to get metrics logging working
- Added a switch --force_1base_probs to ignore 4-base probalities if they exist
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a
- AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface
- Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a
This is a good example for how to untangle a merged BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@269 348d0f76-0448-11de-a6fe-93d51630548a
- HapMapAlleleFrequenciesROD.java - the referenceOrderedDatum implementation
- PrepareROD.java - has a static block that loads the known ROD classes, had to add the above
- GenomeAnalysisTK.java - when supplied a hapmap argument... loads the ROD
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@265 348d0f76-0448-11de-a6fe-93d51630548a
AlleleFrequencyWalker: output the last reference interval if it's left hanging open.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@258 348d0f76-0448-11de-a6fe-93d51630548a
- output GFF lines to a file (specified by a command line argument)
- improve the GFF output string
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@240 348d0f76-0448-11de-a6fe-93d51630548a
walker. Used new command line args for walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@234 348d0f76-0448-11de-a6fe-93d51630548a
still need to add printing GFF intervals for stretches of confident reference calls.
does the GFF ROD class handle intervals?? We'll find out. >:)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@225 348d0f76-0448-11de-a6fe-93d51630548a
All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a
they don't appear to break single sample:
Allele Frequency Metrics (LOD >= 5)
-------------------------------------------------
Total loci : 9000
Total called with confidence : 8138 (90.42%)
Number of variants : 11 (0.14%) (1/739)
Fraction of variant sites in dbSNP : 81.82%
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@192 348d0f76-0448-11de-a6fe-93d51630548a
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