A Detection and Visualization Tool
   for Genomic Variants

Kwang Su Jung1, Kiejung Park1, Sanghoon Moon2, Young Jin Kim2, Bong-jo Kim2

1 Division of Bio-Medical informatics, Cente for Genome Science,Korea National Institute of Health
2 Division of Structural and Functional Genomics, Center for Genome Science, Korea National Institute of Health


freely distributed to public users and private institutions at


Contact: Kwang Su Jung (


Distribution: Download Genovar


Quick User Guide: Download Guide


Test files for detecting Copy Number Variation

Array CGH file
Probe and gene mapping file


Example Sequence Alignment Results (*.bam, *bai) on 1000 genomes :BAM file and its index


UCSC reference sequence file hg 19(GRCh 37) :FastA format
Indices of reference sequence files


Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals.



A JAVA-based stand-alone program called Genovar, which utilizes the Smith-Waterman Array (SW-ARRAY) algorithm to detect CNV regions, was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files.



Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. Genovar is available for download from theGenovar website (




Screen shots

Figure 1. Chromosomal view and statistical summary .