Installation¶
Dependencies¶
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 | |
| Picard | |
| IndelRealignment | GATK |
| BaseRecalibration | |
| Variant Calling | |
| Joint Genotyping | |
| Miscellaneous | Samtools, and |
| Novosort |
Workflow Installation¶
Simply, clone the repository:
git clone https://github.com/ncsa/Swift-T-Variant-Calling/
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