This article is part of the supplement: Seventh International Conference on Bioinformatics (InCoB2008)

Open Access Research

VarDetect: a nucleotide sequence variation exploratory tool

Chumpol Ngamphiw1, Supasak Kulawonganunchai2, Anunchai Assawamakin3, Ekachai Jenwitheesuk1 and Sissades Tongsima1*

Author Affiliations

1 Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phaholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand

2 Department of Computer Science, School of Engineering and Technology, Asian Institute of Technology, P.O. Box 4, Klong Luang, Pathumthani 12120, Thailand

3 Division of Medical Genetics, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand

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BMC Bioinformatics 2008, 9(Suppl 12):S9  doi:10.1186/1471-2105-9-S12-S9

Published: 12 December 2008



Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs associated with predisposing genes in complex diseases. Accurate detection of SNPs requires software that can correctly interpret chromatogram signals to nucleotides.


We present VarDetect, a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces. Accurate SNP base-calling is achieved using pre-calculated peak content ratios, and is enhanced by rules which account for common sequence reading artifacts. The proposed software tool is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) using fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 two-pooled DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency.


VarDetect is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at webcite.