ebanks
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78a4d8ec3d
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Removing more references to VCFRecord
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3790 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-14 16:34:15 +00:00 |
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ebanks
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6b5c88d4d6
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The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3786 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-14 04:56:58 +00:00 |
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ebanks
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fb717fe128
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First pass needed to remove old VCF code: moving all VCF-related constants into a single unified class
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3759 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-11 07:19:16 +00:00 |
rpoplin
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67f1589652
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--fdr_filter_level isn't mandatory
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3748 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-08 22:48:30 +00:00 |
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rpoplin
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5d39cd5db8
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Added --fdr_filter_level to ApplyVariantCuts so that you can create beautiful tranche plots and also decide which tranche level to filter at. The previous version always filtered at the smallest tranche. The tranche filter names are appropriately added to the VCF header.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3747 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-08 22:44:10 +00:00 |
aaron
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3347d1ca7c
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part one of combining format and info header lines code into a single abstract class for Mark; plus some 'm' removals from access methods for Eric. Adding fixes for CombineVariants next.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3719 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-05 05:57:58 +00:00 |
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rpoplin
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255b036fb5
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Variant Recalibrator MLE EM algorithm is moved over to variational Bayes EM in order to eliminate problems with singularities when clustering in higher than two dimensions. Because of this there is no longer a number of Gaussians parameter. Wiki will be updated shortly with new recommended command.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3704 348d0f76-0448-11de-a6fe-93d51630548a
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2010-07-01 18:51:07 +00:00 |
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rpoplin
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724affc3cc
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Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3590 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-18 17:37:11 +00:00 |
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aaron
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4f00e265a8
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quick update for a change I implemented for Ryan
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3519 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:23:31 +00:00 |
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aaron
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ad98512f6c
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adding changes so that we look at the headers already loaded by the engine for samples and other VCF utils, and not create readers for each file to get them (this caused Tribble to regerenate indices if the index file can't be written to disk).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3518 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:21:12 +00:00 |
depristo
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e2b41082af
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GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-02 22:26:32 +00:00 |
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rpoplin
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290771a8c2
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Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-02 15:03:00 +00:00 |
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rpoplin
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87fe60fe4f
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Fix for Sendu. new Process and p.waitFor() don't seem to work on his farm. Throws an IOException. This was a problem way back with AnalyzeCovariates too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3469 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-02 11:37:10 +00:00 |
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ebanks
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eb25e41111
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minor update to new tribble name
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3462 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-28 20:23:25 +00:00 |
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rpoplin
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522dd7a5b2
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Adding the variantrecalibration classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3459 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-28 18:21:27 +00:00 |