V-Phaser

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V-Phaser is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. V-Phaser combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%.

Credits
Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Computational Biology 8(3):e1002417.

Funding
Support for this tool was provided by the National Institute of Allergy and Infectious Diseases through the Microbial Sequencing Center and Genome Sequencing Center for Infectious Diseases, by grants made by the Bill & Melinda Gates Foundation (awarded to the Ragon Institute), the NIAID-DAIDS (awarded to Ragon Institute), and through internal support at the Broad Institute.