What tool is used for CNV calling? August 08, 2022 17:03 Updated Gencove uses CNVkit in wgs mode to call CNVs from low-pass sequence data. An explanation of the output file formats can be found at the following link. Related articles What is Effective Coverage? Can you share any open-source bioinformatics tools in your production pipelines? How do you impute genotypes when there are no reads at a site? How do you calculate contamination for a sample? How to create a new project?