d01d4fdeb5
Optimized version of produce beagle tool, along with experimental (hidden) support for combining likelihoods depending on estimate false positive rate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5430 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-12 02:06:28 +00:00
bf2e02f472
Generic, easy-to-use variant evaluation Queue script that tests indel and SNP call sets against standard evaluation data sets for sensitivity and specificity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5391 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 18:03:29 +00:00
5c979633f0
Due to a problem in the way that dynamic type selection works, I've added an explicit (temporary) ability to restrict VE to specific variant types (SNPs, INDELs, etc), so that calculations will work when a site has a SNP in dbSNP but is called as an indel, causing the SNP site to mysteriously disappear from the comp track, a huge problem for validation report. VEU updated to allow both dynamic type (old) and just returning everything in the track.
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Also, created a standard Queue script that calculates a suite of standard indel and SNP assessment results. Will be the basis for a general evaluation Queue script with standardized data files for SNPs and Indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5385 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-06 19:31:12 +00:00
146756de79
Class name to reflect actual file name. manySampleUGPerformance now operates on 1000 samples!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5326 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-26 23:36:04 +00:00
fe4aa58d35
Removing unused class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5197 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:22:28 +00:00
6c99dc4dab
Take (partial) ownership of phasing 1000G chr20 calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5147 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 21:49:41 +00:00
94b64ec54a
Moving scala script into analysis directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5047 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 18:42:18 +00:00
b45566760e
intermediate checkin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5045 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 18:39:25 +00:00
41c8552d0a
Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5031 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 12:54:03 +00:00
a463dbcda1
Refactoring the qscript directory; oneoffs, playground, and core
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5017 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 15:23:40 +00:00
depristo
fromer
chartl