The cnv2wiggle.pl perl script will create a bed track for ploidy segments different from 2 and a wiggle plot of the relative coverage. These files can be opened in IGV. This script doesn’t include hypervariable regions. It is a very Simple CNV Variants to wig Converter and BED file generator. It uses the cnvDetailsBeta file to create a wiggle track and the cnvSegments file to create a BED track.
Note: This script is not compatible with genomes processed with Assembly Pipeline v2.0.
Download the tool here.