This workflow can be used to scan samples for any mutations of interest. The input is a csv file with the mutations of interest, a Genbank file for the SNV annotations.
Run this workflow on slurm with run_pipeline.sh.
To make a dry-run run snakemake --dry-run.
Run workflow and then run notebook to get the heatmap with the frequencies of mutations of interest per sample.
SARS-CoV-2 drug resistance mutations were taken from the Standford Database: https://covdb.stanford.edu/drms/3clpro/
They can be formatted in the right way using the notebook: resources/generate_mutations_of_interest_table.ipynb