.Lifted to HapMap 3.3
.Lifted to dbSNP 132 where possible.
.Added the CEU-Trio WEx(hg19) dataset
.Added some options to the pipeline
You can now use :
-dataset WEX
-dataset HiSeq
...
to choose which datasets to run through the pipeline.
You can now without BAQ and indel mask:
-noBAQ
-noMASK
Choose not to run the gold standard comparison analysis:
-skipGoldStandard
Activate the VariantEval walker analysis on the Recalibrated vcf:
-eval
The default behavior is to run exactly like it used to, so this version shouldn't change the way you used to use the pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5004 348d0f76-0448-11de-a6fe-93d51630548a
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
rpoplin
carneiro
kshakir