SV/CNV callers
GATK-SV uses an ensemble of SV discovery tools to produce a raw call set and then integrates, filters, refines, and annotates the calls from these tools to produce a final call set.
The SV calling tools, sometimes referred to as "PE/SR" tools, include:
Depth-based calling of copy number variants (CNVs) is performed by two tools:
While it is possible to omit individual tools from the pipeline, it is strongly recommended to use the default configuration that runs all of them.
As of 2024, most published joint call sets generated with GATK-SV used the tool MELT, a state-of-the-art mobile element insertion (MEI) detector, instead of Scramble. Due to licensing restrictions, we cannot provide a public docker image or reference panel VCFs for this algorithm. The version of the pipeline configured in the Terra workspaces does not run MELT or include MELT calls for the reference panel. However, the Scramble tool has replaced MELT as an MEI caller and should provide similar performance.