ContEst is a tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. Using a Bayesian framework, contamination levels are estimated from array based genotypes and sequencing reads.
Cibulskis, et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics. 2011 Sep 15;27(18):2601-2. Epub 2011 Jul 29.