DIG Aggregator Methods

This is the documentation about aggregator methods.

Quickstart

Every sub-folder in this repo is a completely separate, independent method project for the DIG Aggregator. They can be run from here using one of the run scripts present in the root directory.

# dry run the bottom-line method
$ ./run.sh bottom-line

# run a stage of the bioindex method in test mode
$ ./run.sh bioindex --stage GenesStage --test --yes

You can also simply go into the sub-directory of the method project and run it yourself.

Creating a New Method

After installing SBT, you can instantiate a new method from a Giter8 template in the root directory:

$ sbt new broadinstitute/dig-aggregator-method.g8

Simply enter the name of the new method and change any of the follow-up defaults as desired.

NOTE: On the Broad file system, SBT can be installed with use SBT.

Data Locations

• phenotype stats
  • dataset specific
    • variants/{sequence tech}/{dataset}/{phenotype}/
  • ancestry specific
    • out/metaanalysis/ancestry-specific/{phenotype}/{ancestry}/
  • bottom line across all ancestries
    • out//metaanalysis/trans-ethnic/{phenotype}/