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SNPTools is a suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve highly accurate genotype calling and phasing in an efficient way.

SNPTools paper is online at Genome Research in Jan, 2013:

Wang, Y., Lu, J., Yu, J., Gibbs, R. a, & Yu, F. (2013). An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome research. doi:10.1101/gr.146084.112 abstract

For usage info, please refer [Best practices with SNPTools]
For our best practices of integrated SNP analysis, please refer [Best practices of integrated SNP analysis]

We also tried to setup SNPTools on Amazon cloud, which greatly speedup our processing of 1000 Genomes Phase3 data. For the instruction, please refer [Run SNPTools on Amazon Cloud]