HG002 QC Snakemake
To Run
Resources and data specified within snakefile (hg002QC.smk) for simplicity. Tested with snakemake v6.15.3.
Warning: Several steps of this workflow require minimum coverage. It’s recommended that this workflow not be run when yield in base pairs is insufficient to produceat least 15X coverage (i.e. yield/3099922541 >= 15x).
# clone repo
git clone --recursive https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake.git workflow
# make necessary directories
mkdir cluster_logs
# create conda environment
conda env create --file workflow/environment.yaml
# activate conda environment
conda activate pb-human-wgs-workflow
# submit job
sbatch workflow/run_hg002QC.sh
Plots
A list of