Integrated Platform for Copy Number Variations - Detection, Annotation and Visualization

iCopyDAV enables the user to identify copy number variations (CNV), an important category of structural variants, in whole genome sequence data. The pipeline considers Depth-of-Coverage based approach for CNV detection due to its ability to predict absolute copy number of the variant. The pipeline doesn’t require any matched-control sample and can be used for CNV detection in samples from species other than human (however, functional annotation is available only for human genome assembly hg18/hg19).

Source code: Github link

Docker's image: icopydav.tar

Mappability files: hg18 hg19

GC content score files: hg18 hg19

Genome files: hg18 hg19

Annotations: annotations.tar.gz

Documentation: Manual

Sample file: test.tar

Contact: Prashanthi Dharanipragada, Sriharsha Vogeti and Dr. Nita Parekh,
Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology-Hyderabad, India