Whole Exome

If the samples are whole exome samples, a target BED file should be supplied with the --cnv-target-bed $TARGET_BED option.

The intervals in target BED file indicate regions where alignments are expected based on the target capture kit. The BED file intervals are further split into intervals of smaller size, depending on the value of cnv-interval-width.

To use a standard BED file, make sure that there is no header present in the file. In this case, all columns after the third column are ignored, similar to the operation of DRAGEN Variant Caller.