/mngvariants

MicrobesNG variant calling.

Primary LanguagePython

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