PyClone is a tool for inferring the cellular prevalence of point mutations from deeply sequenced data. The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose cellular prevalences shift together. Such clusters of mutations can be inferred as mutational genotypes of distinct clonal populations. The model is described and evaluated in the following publication:
Bouchard-Côté A, Shah SP. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014 Apr;11(4):396-8. doi: 10.1038/nmeth.2883. Epub 2014 Mar 16. PubMed PMID: 24633410.
An early version of this software was used to produce the results reported in Shah et al. (2012):
Installation and Use
Please visit the project page https://bitbucket.org/aroth85/pyclone for the most up to date instructions.
Software download here.
A user group has been established at: https://groups.google.com/forum/#!forum/pyclone-user-group . Please be sure to join the group and post any questions/comments/bugs/issues to the forum.