A quick & dirty code to call variants in bacterial genomes

You have one or multiple newly sequenced bacterial draft genomes, sampled or cultured under different conditions, and want to call the SNPs against a reference genome to find phenotype-associated variants? Well, here it is a quick & dirty way to do so!

Requirements

Get or install:

1. bwa
2. samtools
3. bcftools
4. seqtk
5. Trimmomatic
6. Their dependencies

Run

Make it executable:

sudo chmod +x variant_call.sh

Run it:

./variant_call.sh