This repository contains Pairtree input files and analysis script for "Colorectal cancer cells possess an equipotent capacity to enter a reversible diapause-like state to survive chemotherapy" with Sumaiyah Rehman, ..., Catherine O'Brien.
Jeff Wintersinger performed this analysis.
inputs.nocna.separated: input files split into separate samples, containing only mutations from diploid regions for each sample individually
inputs.nocna.combined: input files split into separate samples, containing only mutations from the intersection of diploid regions across samples. Mutations absent from a sample are given zero variant reads, and a total number of reads corresponding to however many reads were present at that genomic locus.