Variant Calling (Part 1): Building a Reproducible GATK Variant Calling Bash Workflow with Pixi
· 19 min read
This blog is designed as a practical starting point for building bioinformatics workflows focused on germline variant calling. You'll begin with a straightforward, standard approach using bash and reproducible environments. In future posts, we'll explore how to transition to best-practice workflow management with Nextflow, allowing for further optimization, customization, and integration of additional tools to enhance workflow quality.