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 program is used for genotype imputation? Can you share any open-source bioinformatics tools in your production pipelines? Gencove Imputation What is Effective Coverage? Gencove Technical Docs