TMB calculator

tumor mutational burden calculation method that works ONLY for a custom MGPT (with a given number of sequenced loci)

This tool calculates the Tumor Mutational Burden (TMB) from a provided SQLite database. The TMB is calculated as the number of non-synonymous coding variants per megabase (Mb) of the examined sequence.

about TMB

Tumor Mutational Burden (TMB) is an emerging, independent predictive biomarker of immunotherapies in multiple tumor types. It measures the number of mutations within a tumor genome and can offer insight into the likelihood of a patient's response to immunotherapies.

The SQLite database should contain a table named variant with at least the following columns:

• base__coding: Indicates whether the variant is coding (with value 'Y') or not.
• base__so: The type of the variant. Non-synonymous coding variants are those that are not of type 'SYN' or 'INT'.

python tmb_calculator.py [DATABASE_FILE]

Using Docker

Pulling the Docker Image

Pull the Docker image from the repository:

docker pull alperakkus/mutationalburden:latest

docker run -v /local/path:/data alperakkus/mutationalburden:latest /data/YOUR_DATABASE_FILE.sqlite

This project is licensed under the MIT License.