afrangou / CleanCNA

An R package to classify a copy number call as of high or low quality, to re-estimate purity and ploidy parameters based on a set of collected metrics, and to iteratively rerun the copy number calling process to provide a high quality set of copy number calls using WGS data.

CleanCNA

Calling subclonal copy number aberrations (CNA) with Battenberg, DPClust, and iterative recalls to provide a high quality and reproducible set of copy number calls.

Battenberg calls subclonal copy number using germline mutation information (SNPs), DPClust then clusters somatic mutations (SNVs) by cancer cell fraction (CCF) using the copy number information from Battenberg. Metrics are calculated to assess the accuracy of the copy number call. Adjusted purity (ρ) and ploidy (ψ) parameters are calculated if required, and the copy number profile is iteratively refitted where necessary. Detailed metrics for inclusion or exclusion of samples is provided.