Welcome to the MARVELous documentation
MARVELous (Marion’s Analysis of Rare Variant Effects in Large data) is a Python toolkit for associating phenotypes with carriership of genetic variants.
The package performs variant extraction from genetic files (VCF, BGEN, PLINK) and statistical association testing with various outcome types.
Getting Started
Examples
API
Project Admin
- Contributing to the project
- Adding New Config Options to MARVEL
- Overview
- Step 1 — Add the option key to
constants.py - Step 2 — Add the field to
PipelineConfig - Step 3 — Add validation to
check_config_file() - Step 4 — Use the option in the pipeline
- Step 5 — Update the example config file
- Step 6 — Update the constants docstring / reference table
- Step 7 — Write tests
- Quick-reference checklist
- Config file format reference
- Worked example — adding a
min_acallele-count filter
- Raising issues