Structural Variant VCF Output

The structural variants VCF output file is available in the output directory. The file is named <output-file-prefix>.sv.vcf.gz. The contents of the file depend on the type of analysis.

For each major analysis category (germline, tumor/normal and tumor-only), the appropriate VCF output file is output, reflecting variant calls made under the variant calling mode corresponding to the given analysis type.

The Structural Variant caller produces additional output in the <output-directory>/sv/ directory. The <output-directory>/sv/results folder contains additional variants and statistics output files. Additional subdirectories contain logs and intermediate outputs from the variant calling process.