denovo-variant-examples

Examples of running denovo-variant-caller on GCE instances

To get a list of all the options :

$ fab -l -f src/scripts/fabfile.py
Available commands:

    create_denovo_instances      Create new denovo instances
    delete_all_denovo_instances  Deletes all denovo instances
    delete_instance              Deletes a particular instance by name
    list_denovo_instances        Lists all the denovo instances
    list_instances               Lists all the instances in my GCE

Creating GCE instances

Create a new denovo instance :

$ fab -f src/scripts/fabfile.py create_denovo_instances
Creating instances...
Creating disk denovo-1
Creating instance denovo-1

Done.

Create several instances with 4 cores each :

$ fab -f src/scripts/fabfile.py create_denovo_instances:num_instances=2,num_cores=4
Creating instances...
Creating disk denovo-2
Creating instance denovo-2
Creating disk denovo-3
Creating instance denovo-3

Done.

List all the denovo instances :

$ fab -f src/scripts/fabfile.py list_denovo_instances
denovo-1
denovo-2
denovo-3

Done.

Delete instance denovo-1 :

$ fab -f src/scripts/fabfile.py delete_instance:denovo-1
Deleting instance : denovo-1...

Done.

Delete all denovo instances :

$ fab -f src/scripts/fabfile.py delete_all_denovo_instances
Deleting all denovo instances...
Are you sure? (y|n): y
Deleting instance : denovo-2...
Deleting instance : denovo-3...

Done.

Running Denovo Variant Caller

Run stage 1 over chromosome1:

Run stage 1 over chromsome2 ;

Run stage 2 :