MicrobesNG Variant Calling

Installation

1. Create a file mngvariants/.env to store the required environment variables
2. Run pip install -U . at the repo root to install as a package
3. The command mngvariants will now be available

External Dependencies

The following external dependencies are required and can be installed using Anaconda from the Bioconda channel:

• bwa@0.7.17
• samtools@1.9
• snpeff@4.3.1t
• varscan@2.4.3