jgoecks / somatic-variants

Processing variants to find somatic variants without a matched normal.

Creating a complete GEMINI database

1. Modify settings/paths in gemini/default_settings
2. Make sure requirements in gemini/create_gemini_db.sh
3. Run gemini/create_gemini_db.sh

Querying an RCC GEMINI database for somatic variants.

NOTE: for script to run, your PYTHONPATH must include GEMINI; see gemini/default_settings.sh for an example.

1. Modify settings/paths in gemini/default_settings
2. Run PYTHONPATH=/path/to/gemini python /this/directory/gemini/rcc.py to see options for filtering variants
3. 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'
4. 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