20f29e4690
In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4941 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 20:30:55 +00:00
7185fcb47b
Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4891 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 21:14:20 +00:00
4ca1da1d07
Updating the NA12878.HiSeq bam file to be the correct bam file in the methods development qscript.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4879 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 14:53:10 +00:00
8fac346ac1
Misc cleanup in Methods Development Qscript
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4878 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 04:24:25 +00:00
34ab5b4889
Turning on BAQ in Methods Development pipeline. A new dataset is added: 363 EUR samples from the November 1000G release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4877 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-19 21:13:25 +00:00
15a33545f4
Updating Methods development pipeline qscript with the bam lists for all the data sets. It is ready for people to start running with it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4875 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 22:19:14 +00:00
bdef4e775a
Initial checkin of methods development pipeline qscript. It allows the methods dev team to run an overnight job which calls and recalibrates a variety of data sets and allows for an end-to-end sanity check of final results for potential changes to the methods. It isn't meant to be used by anybody quite yet, but shows the general structure and flow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4871 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:14:02 +00:00
095fc1922a
By popular demand I'm adding the qscript I used to do the 660 bamfile 1000G calling for ASHG. It does cleaning, BAQing, and merging in 3mb chunks genome-wide then calls SNPs on those temporary bams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4866 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 18:49:03 +00:00
fd5970fdd4
At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.
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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
2010-09-02 21:30:48 +00:00
4f51a02dea
Changed logging level to default at INFO instead of WARN.
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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
2010-08-09 16:42:48 +00:00
87470d5fe5
Checking in a simplistic VR qscript file for posterity's sake
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3705 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 18:53:17 +00:00
rpoplin
kshakir