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SequenzaSequenzacancer NGS data analysisSequenza is a novel set of tools providing a fast python script to genotype cancer samples, and an R package to estimate cancer cellularity, ploidy, genome wide copy number profile and infer for mutated alleles. sequenza-utils PythonGetting Help
Mailing list at Google Groups - User Guide
Cellularity and ploidy estimationThe cellularity and ploidy values of the sample are estimated trough Bayesian inference. The results can be expressed in a selected confidence region (C.R.) and one point estimate. Copy number and mutations profileThe sequenza R package uses the estimated value of cellularity and ploidy to fit the data into the built-in model, estimating copy number and mutated allele from the data. Furthermore the package provides very intuitive, yet information rich graphics 
Genome wide profilingCopy number and allele composition, genome wide profiles 
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