...
...
...
...
|
This page shows you how to run GATK4 using our recently installed Singularity GATK4 container. The runAsPipeline script, accessible through the rcbio/1.0 module, converts the bash script into a pipeline that easily submits jobs to the Slurm scheduler for you.
...
The workflows are downloaded from: https://github.com/gatk-workflows/gatk4-data-processing and https://github.com/gatk-workflows/gatk4-somatic-snvs-indels
Jump start
Here are the commands to test out the workflow using example data. The whole run need a few hours if the cluster is not busy.
...