Technical Details

This section describes a little more details on the inner workings of MOMA, including the various filtering and annotation steps and the necessary resources to generate the final report. It is helpful to consult the flow diagram at the beginning of this document (MOMA Workflow) to get a better sense of how the data flows and what is happening at each step.

Briefly, we can break the flow of data down into a few components:

  1. VCF Parsing and preparation for Annovar
  2. Annovar annotation
  3. MAF file generation
  4. MOMA MOI / VuS Annotation
  5. Reporting

As the flow diagram shows, there certainly are other steps and components that occur during a run. But, these 5 are the main components leading to a final result.

Pipeline Organization

The MOMA pipeline is constructed of a series of Perl, Python, and BASH scripts that all work together to work the data through the flow described above. These scripts can be categorized as helper scripts used to modify the data in a way the pipeline can use it, pipeline scripts that shunt the data through the various paths in the workflow, and analytical scripts that generate data. Most of these scripts are all stored within the scripts/ directory in the package root.

MOI Annotation Rules

Mutations of interest (MOIs) are defined as variants that have an oncogencity rating per OncoKB annotation. Per OncoKB’s website, “OncoKB contains detailed information about specific alterations in 671 cancer genes.”