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Code used to generate Genome In A Bottle CMRG benchmark sets

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GIAB CMRG Code Base

Code used to generate the Complex Medically Relevant Genes benchmark sets.

Pipeline dependencies are available as conda packages, including jupyter notebook with a bash kernel to run the pipeline in the jupyter notebooks. The required packages are are defined inenvironment.yml.

Create the conda env (can also use mamba, a faster implementation of the conda package manager).

conda env create --name cmrg_benchset --file environment.yml

Pipelines are run in ipython notebooks using the bash kernel

conda activate cmrg_benchset

## Use ipython notebook for bash kernel
ipython notebook

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Code used to generate Genome In A Bottle CMRG benchmark sets

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