musta

A novel affordable and reliable framework for accurate detection and comprehensive analysis of somatic mutations in cancer

Contents

• Overview
• Requirements
• Quick Start

Overview

Accurate detection and comprehensive analysis of somatic variants are a major task in cancer sample data analysis, which is routinely carried out combining different software packages with specific software dependencies and with the need of laborious and time-consuming data format conversions.

To overcome these limitations, we developed Musta, an end-to-end pipeline to detect, classify and interpret mutations in cancer.

Musta is a Python command-line tool that easily handles matched tumour-normal, from variant calling to the deconvolution of mutational signatures, through variant annotation, driver genes detection, pathway analysis, tumor heterogeneity.

Musta's core is Snakemake-based and was conceived for an easy installation through the Docker platform. A simple Makefile bootstraps Musta, taking care of the installation, configuration and running steps and allowing the execution of the entire pipeline or any individual step depending on the starting data.

Musta is currently used for cancer sample data analysis at the CRS4-NGS Core

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Requirements

To install and run Musta, it is essential to have Docker installed on your computer. Docker is a containerization platform that ensures consistency and compatibility in running Musta across different computing environments.

If you do not have Docker installed, you can download and install it by following the instructions provided in the official Docker documentation: Docker Installation Guide.

Please ensure that Docker is properly configured and running on your system before proceeding with the installation of Musta.

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Quick Start

The installation process may take several minutes.

1. Clone the repository:

   git clone https://github.com/next-crs4/musta.git

2. Change into the Musta directory:

   cd musta

3. Initialize the Musta framework:

   make bootstrap

4. Confirm the Musta Docker image has been built:

   docker images

   You should see an output similar to:

   REPOSITORY   TAG          IMAGE ID         CREATED       SIZE
   musta        Dockerfile   bb170cfc6546     2 hours ago   2.48GB
   

   This indicates the Musta Docker image is successfully built.

5. Verify the Musta Command Line Interface (CLI) installation:

   musta --help

   You should see an output like this:

   usage: musta [-h] [--config_file PATH] [--logfile PATH]
                [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                {detect,classify,interpret} ...
   
   End-to-end pipeline to detect, classify and interpret mutations in cancer
   
   optional arguments:
     -h, --help            show this help message and exit
     --config_file PATH, -c PATH
                           configuration file
     --logfile PATH        log file (default=stderr)
     --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                           logger level.
   
   subcommands:
     valid subcommands
   
     {detect,classify,interpret}
                           sub-command description
       detect              Somatic Mutations Detection.
                               1.  Multiple Variant Calling: mutect, lofreq, varscan, 
                                   vardict, muse, strelka.
                               2.  Ensemble consensus approach to combine results and 
                                   to improve the performance of variant calling
       classify            Variant Annotation
                           Functional annotation of called somatic variants 
                           
       interpret           Somatic Mutations Interpretation:
                               1.  Identification of cancer driver genes 
                               2.  Check for enrichment of known oncogenic pathways.
                               3.  Infer tumor clonality by clustering variant allele frequencies.
                               4.  Deconvolution of Mutational Signatures
   

   This indicates the Musta CLI is correctly installed and ready for use. You can now proceed with using Musta for somatic mutation analysis in cancer research by following the instructions provided in the User Guide.

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