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