Variant calling workflow using GATK4

For now, for simplicity, we assume that each sample is a 'platform unit'.

Usage

1. Fill out/Edit the bin/config.yaml file.

2. Make samplesheet. You can go to the bin/ folder and run bash make_samples_template.sh. Rename the output file samples_template.tsv as samples.tsv.

3. A file named grouped_contigs.tsv with a column named 'name' and a second column named 'contigs' containing comma-delimited sequence names (chromosome/contig names) is needed. You may first load a R module by running module load bbc2/R/alt/R-4.2.1-setR_LIBS_USER, then run Rscript group_contigs.R to generate this file based on the reference sequence listed in config.yaml.

4. Submit job with sbatch -p <parition name: e.g., long or bbc> bin/run_snakemake.sh.

Workflow