andrewk
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4e7e0432a2
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Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2378 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-16 20:44:30 +00:00 |
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andrewk
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bf76019f22
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Minor change to coverage evalution script, to update for new file format and add output fields
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2375 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-16 18:06:08 +00:00 |
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andrewk
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d191e02c88
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Automated parsing stats from VariantEval and outputting stats to "*.oneline_stats" files; needed to do larger culling of predictions vs. actual SNP call for Pilot 3 lanes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1620 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-14 23:40:11 +00:00 |
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andrewk
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1c648a2d5f
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Skip compiled python files (*.pyc) in svn status output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1346 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-30 21:45:23 +00:00 |
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andrewk
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00f9bcd6d1
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CoverageEval.py tool right before some major changes to the core of the code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1293 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-22 16:58:23 +00:00 |
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andrewk
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c8fcecbc6f
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Added ParseDCCSequenceData.py to repository and made changes that allow an analysis of quantity of sequence data by platform and project, moved table / record system to a new module called FlatFileTable.py and built that into ParseDCCSequenceData and CoverageEval.py; changed lod threshold in CoverageEvalWalker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1201 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 22:04:26 +00:00 |
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andrewk
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d3daecfc4d
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Added unit tests for function in ListUtils to randomly sample lists with replacement, updated AlleleFrequencyEstimate to provide a callType of HomRef, HetSNP, HomSNP, update indices in CoverageEval.py, and made a lot of changes to CoverageWalker biggest one being that it directly calls SingleSampleGenotyper instead of implementing some parts of SSG itself.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1189 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 02:05:40 +00:00 |
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andrewk
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dcb8892568
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Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1162 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-03 08:07:02 +00:00 |