# Generic variant calling A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs: - A genbank file with the reference genomes - A collection of paired fastqsanger files The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the [Reporting workflow](https://workflowhub.eu/workflows/354). Workflow can be accessed directly on [usegalaxy.org](https://usegalaxy.org/u/aun1/w/generic-variation-analysis-on-wgs-pe-data) The general idea of the workflow is: 