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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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rpoplin 5623e01602 GenerateVariantClusters and VariantRecalibrator now uses hapmap and 1kg ROD bindings (in addition to dbsnp) to distinguish between knowns and novels. It no longer looks at by-hapmap validation status so providing hapmap is highly recommended. Example on the wiki. Input variants tracks now must start with input. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4113 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-25 18:33:40 +00:00
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annotator Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
coverage Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
fasta Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
filters Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
genotyper Forgot to update UG performance test to reflect the new -o argument. 2010-08-23 00:57:16 +00:00
indels Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
qc Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
recalibration Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
sequenom Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
varianteval Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax 2010-08-25 03:47:57 +00:00
variantrecalibration GenerateVariantClusters and VariantRecalibrator now uses hapmap and 1kg ROD bindings (in addition to dbsnp) to distinguish between knowns and novels. It no longer looks at by-hapmap validation status so providing hapmap is highly recommended. Example on the wiki. Input variants tracks now must start with input. 2010-08-25 18:33:40 +00:00
variantutils Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
PileupWalkerIntegrationTest.java Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
PrintReadsWalkerUnitTest.java Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting. 2010-08-22 14:27:05 +00:00
VariantsToVCFIntegrationTest.java Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00