Changes

[[File:GotCloudDiagram.png]]

[[File:GotCloudDiagram.png]]

[[GotCloud]] incorporates the alignment and variant calling pipelines into one easy to use tool.  GotCloud can run on a user's computer, on an instance in a compute cloud, and can even split the work up onto a cluster of machines or instances.  This tutorial is just a small test that just runs on the machine the commands are run on.

[[GotCloud]] incorporates the alignment and variant calling pipelines into one easy to use tool.  GotCloud can run on a user's computer, on an instance in a compute cloud, or can split the work up onto a cluster of machines or instances.  This tutorial is just a small test that just runs on the machine the commands are run on.

== STEP 1 : Setup GotCloud ==

== STEP 1 : Setup GotCloud ==

== STEP 6 : Run GotCloud Association Analysis Pipeline ==  

== STEP 6 : Run GotCloud Association Analysis Pipeline ==  

  /net/fantasia/home/hmkang/bin/epacts/bin/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped --out EPACTS_TEST --test q.linear --run 1 --top 1 --chr 20  

  /net/fantasia/home/hmkang/bin/epacts/bin/epacts single --vcf $GCOUT/vcfs/chr20/chr20.filtered.vcf.gz --ped $GCDATA/test.GBR60.ped --out EPACTS_TEST --test q.linear --run 1 --top 1 --chr 20

= Tutorial Inputs =  

= Tutorial Inputs =