MicrobesNG Variant Calling
Installation
- Create a file
mngvariants/.env
to store the required environment variables - Run
pip install -U .
at the repo root to install as a package - 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