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 http://www.biotec.or.th/GI/tools/vardetect.
Posted on 07 May 2009.