- Modify settings/paths in
gemini/default_settings
- Make sure requirements in
gemini/create_gemini_db.sh
- Run
gemini/create_gemini_db.sh
NOTE: for script to run, your PYTHONPATH must include GEMINI; see gemini/default_settings.sh
for an example.
- Modify settings/paths in
gemini/default_settings
- Run
PYTHONPATH=/path/to/gemini python /this/directory/gemini/rcc.py
to see options for filtering variants - Example usage:
PYTHONPATH=/path/to/gemini python /this/directory/gemini/rcc.py find_somatic --gemini-db my_variants.db --min-allele-freq 0.05 --min-alt-depth 5 --min-depth 20 --sample-pattern FL01'
- Augment results with joint columns and num_het_by_id, fix num_het:
PYTHONPATH=/path/to/gemini python /this/directory/gemini/rcc.py augment_vars --results-file find_somatic_results_FL01_minaf0.05_ad5_d20.txt