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The main page is http://genome.sph.umich.edu/wiki/GotCloud .
The main page is http://genome.sph.umich.edu/wiki/GotCloud .
Pages that document or help with installation:
* http://genome.sph.umich.edu/wiki/GotCloud:_Binary_Releases
* http://genome.sph.umich.edu/wiki/GotCloud:_Binary_Releases
* http://genome.sph.umich.edu/wiki/GotCloud:_Source_Releases
* http://genome.sph.umich.edu/wiki/GotCloud:_Source_Releases
** http://genome.sph.umich.edu/wiki/StarCluster
** http://genome.sph.umich.edu/wiki/StarCluster
Pages that document steps in the GotCloud pipeline:
* http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline
* http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Pipeline
** http://genome.sph.umich.edu/wiki/GotCloud:_Alignment_Sub-Pipelines
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Pipeline
* http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options
** http://genome.sph.umich.edu/wiki/GotCloud:_Variant_Calling_Options (sub-page)
* http://genome.sph.umich.edu/wiki/GotCloud:_GenomeSTRiP_Pipeline
* http://genome.sph.umich.edu/wiki/GotCloud:_Creating_a_New_Pipeline
Pages that document pieces of GotCloud:
* http://genome.sph.umich.edu/wiki/PileupBasedVariantCalling
* http://genome.sph.umich.edu/wiki/GotCloud:_Filters
* http://genome.sph.umich.edu/wiki/GotCloud:_Filters
* http://genome.sph.umich.edu/wiki/VcfCooker
* http://genome.sph.umich.edu/wiki/Understanding_VerifyBamID_output
* http://genome.sph.umich.edu/wiki/Understanding_QPLOT_output
* http://genome.sph.umich.edu/wiki/Understanding_vcf-summary_output
* http://genome.sph.umich.edu/wiki/GotCloud:_Genetic_Reference_and_Resource_Files (documentation and instructions)
Pages that explain configuration:
* http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers <code>BATCH_OPTS</code>)
* http://genome.sph.umich.edu/wiki/Configure_GotCloud (mainly covers <code>BATCH_OPTS</code>)
Tutorials:
Tutorials:
* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo
* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo
* http://genome.sph.umich.edu/wiki/GotCloud:_Amazon_Demo_Setup
* http://genome.sph.umich.edu/wiki/Tutorial:_Low_Pass_Sequence_Analysis
Pages for developers:
Pages for developers:
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud
* http://genome.sph.umich.edu/wiki/Releasing_GotCloud
* http://genome.sph.umich.edu/wiki/Git_FAQs
* http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2
* http://genome.sph.umich.edu/wiki/Creating_an_AMI_on_EC2
Other pages:
* http://genome.sph.umich.edu/wiki/GotCloud:_FAQs
* http://genome.sph.umich.edu/wiki/GotCloud:_Versions documents old versions
Event-specific pages:
Event-specific pages:
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud_UW_CMG
* http://genome.sph.umich.edu/wiki/Short_Workshops links to all of them (or their parents)
Pages that ought to be hidden or deleted:
Pages of which some ought to be hidden, deleted, or heavily re-worked:
* http://genome.sph.umich.edu/wiki/GotCloud:_RedHat_Package
* http://genome.sph.umich.edu/wiki/GotCloud:_RedHat_Package
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud
* http://genome.sph.umich.edu/wiki/Tutorial:_GotCloud
* http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2
* http://genome.sph.umich.edu/wiki/Creating_a_Snapshot_on_EC2
* http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (<code>FA_REF</code> has since been renamed.)
* http://genome.sph.umich.edu/wiki/GotCloud:_Reference_Files (<code>FA_REF</code> has since been renamed.)
* http://genome.sph.umich.edu/wiki/UMAKE
* http://genome.sph.umich.edu/wiki/Mount_S3_Volume
* http://genome.sph.umich.edu/wiki/GotCloud:_AMIs
* http://genome.sph.umich.edu/wiki/GBR60vc.conf
