ContEst

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.  

 

More information about the algorithm is presented in our Bioinformatics paper, availabe here:

http://bioinformatics.oxfordjournals.org/content/early/2011/07/29/bioinformatics.btr446.abstract

For help with ContEst, please email contest-help@broadinstitute.org