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gatk-3.8/java/src/org/broadinstitute/sting
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depristo 4759fdd2ac V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4637 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-08 21:01:33 +00:00
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alignment Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
analyzecovariates All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException. 2010-09-10 15:25:30 +00:00
commandline Cleanup for multithreading memory leak during integration tests...unregister MXBean at end 2010-10-28 18:37:42 +00:00
datasources/pipeline Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
gatk V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R 2010-11-08 21:01:33 +00:00
oneoffprojects V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R 2010-11-08 21:01:33 +00:00
playground Found the cause of 80% of our non-called FNs: an excess of filtered bases were causing us to choose the wrong alternate allele. More details to dev team. 2010-11-07 03:39:57 +00:00
queue There's no such thing as a sam index, so the GATK extension generator doesn't need to add an @Input for them. 2010-10-27 20:39:03 +00:00
utils V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R 2010-11-08 21:01:33 +00:00