First, you need Swift/T installed in your system. Depending on your system, the instructions below will guide you through the process:

Next, depending on the analysis step you like, you also need the installation path of the following tools in your system:

Step Tool options
Alignment Bwa mem or Novoalign
Sorting Novosort
Marking Duplicates Samblaster,
Novosort, or
IndelRealignment GATK
Variant Calling
Joint Genotyping
Miscellaneous Samtools, and

Workflow Installation

Simply, clone the repository:

git clone

Additionally, you may need R installed along with the following packages shiny, lubridate, tidyverse and forcats. Detailed instructions are on the Logging functionality section of the User Guide