Experiment with different indexes for variant storage

[ronammar]

As discussed in our meeting, variant documents should be indexed by the fields that will be used to filter them.

Proposed variant collection indexes:

• chromosome, position
• all AF annotations
• effect annotation (not sure exact syntax for annovar)

Also, does in adding the variant index speed up querying? Does MongoDB automatically create an index? Is the default indexing adequate for quick querying?

[ronammar]

Tested, and we explored using or dropping indexes