DPClust

This R package contains methods for subclonal reconstruction using variant allele frequencies (VAFs) of SNVs and/or indels from whole genome, whole exome or targeted sequencing data. If provided with purity and copy number estimates from a copy number caller such as Battenberg, it will adjust VAFs to cancer cell fractions (CCFs), allowing the clustering of all mutations. The methods were originally described in The Life History of 21 Breast Cancers.