Introducing new automate SNP detection software: VarDetect

VarDetect is 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. This software provides an accurate detection of SNPs, which is a crucial step to identify mutations in monogenic diseases.

In the recent study published in BMC Bioinformatics 2008, 9(Suppl 12):S9, VarDetect is benchmarked against four other well-known SNP discovery software tools (PolyPhred, novoSNP, Genalys and Mutation Surveyor) analyzing fluorescence based chromatograms from 15 human genes. These chromatograms were obtained from sequencing 16 pooled (two) DNA samples; a total of 32 individual DNA samples. In this comparison of automatic SNP detection tools, VarDetect achieved the highest detection efficiency.


VarDetect was developed by Biostatistics & Informatics Laboratory, BIOTEC's Genome Institute. It was written in Java; hence it is compatible with most major operating systems such as Microsoft Windows, Linux, and Mac OSX. The current version of VarDetect is freely available at


Posted on 07 May 2009.