WDL Analysis Research Pipelines

Cloud-based scalable and efficient single-cell genomics workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Detect clonal haematopoiesis of indeterminate potential (CHIP) mutations using the GATK4 Mutect2 somatic variant calling pipeline and the Cromwell workflow engine.

WDL and docker image for running BatVI

WDLs for the Single Sample GATK-SV pipeline

Workflow to generate consensus sequence bases on UMIs using consensusCruncher.