HD-CNV: hotspot detector for copy number variants.

Authors

Jenna L Butler, Department of Computer Science, The University of Western Ontario, London, ON, Canada N6A 3K7
Marjorie Elizabeth Osborne Locke, Department of Computer Science, The University of Western Ontario, London, ON, Canada N6A 3K7
Kathleen A Hill, Department of Computer Science, The University of Western Ontario, London, ON, Canada N6A 3K7 & Department of Biology, The University of Western Ontario, London, ON, Canada N6A 5B7
Mark Daley, Department of Computer Science, The University of Western Ontario, London, ON, Canada N6A 3K7 & Department of Biology, The University of Western Ontario, London, ON, Canada N6A 5B7

Document Type

Article

Publication Date

1-15-2013

Journal

Bioinformatics (Oxford, England)

Volume

29

Issue

2

First Page

262

Last Page

263

URL with Digital Object Identifier

10.1093/bioinformatics/bts650

Abstract

SUMMARY: Copy number variants (CNVs) are a major source of genetic variation. Comparing CNVs between samples is important in elucidating their potential effects in a wide variety of biological contexts. HD-CNV (hotspot detector for copy number variants) is a tool for downstream analysis of previously identified CNV regions from multiple samples, and it detects recurrent regions by finding cliques in an interval graph generated from the input. It creates a unique graphical representation of the data, as well as summary spreadsheets and UCSC (University of California, Santa Cruz) Genome Browser track files. The interval graph, when viewed with other software or by automated graph analysis, is useful in identifying genomic regions of interest for further study.

AVAILABILITY AND IMPLEMENTATION: HD-CNV is an open source Java code and is freely available, with tutorials and sample data from http://daleylab.org.

CONTACT: jcamer7@uwo.ca