VAAL (Variant Ascertainment ALgorithm) is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achieves very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others.
Computational R&D, The Broad Institute, Cambridge, MA
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Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Jan 2009.
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Nature Methods 6: 67–9.