Running a bamsurgeon workflow


bamsurgeon is a tool that will introduce genomic variants (such as SNV, SV, and indel mutations) into BAM, CRAM, and SAM files. The resulting mutated BAM files can be used to test variant callers.

About the Workflow
Bamsurgeon was originally developed by Adam Ewing. This workflow adapts the original Dockerfile and python scripts to work with a WDL on Terra. All scripts that are used in the tasks of this workflow can be found on

This is a companion discussion topic for the original entry at