Somatic Callable Regions Report

In somatic mode, DRAGEN automatically generates a somatic callable regions report as a bed file. The somatic callable regions report includes all regions with tumor coverage at least as high as the tumor threshold and (if applicable) normal coverage at least as high as the normal threshold. If only the tumor sample is provided, then the report includes all regions with tumor coverage at least as high as the tumor threshold. Each line in the bed output file is formatted as follows.

chromosome region_start region_end

You can specify the threshold values using the --vc-callability-tumor-thresh or --vc-callability-normal-thresh options. The default value for the tumor threshold is 15. The default value for the normal threshold is 5. For more information on each option, see Somatic Mode Options.

If the target bed or the --qc-region-coverage-region-i (where i is 1, 2, or 3) option is included in the run. DRAGEN then generates corresponding somatic callable regions bed files in addition to the whole genome somatic callable region bed file.