Swift_T_Variant_Calling’s documentation!

Welcome to this documentation site for a complete Variant Calling pipeline written in Swift/T. This guide leads you through the workflow in terms of what it does, and how to up and running in using it.

The pipeline has been implemented according to the GATK’s best practices for germline variant calling in Whole Genome and Whole Exome Next Generation Sequencing datasets, given a single sample or a cohort of samples, paired- or single-end reads with flexibility in choosing analysis stages, software tools and their versions, and their individual parameters for the specific analysis scenario.