To run some of the scripts provided here, SCAN2 output is necessary. SCAN2 v0.9 produces R data files (.rda) in snv/[sample_ID]/somatic_genotypes.rda and indel/[sample_ID]/somatic_genotypes.pon_filter.rda. These files must be made deposited in scan2_somatic_genotype_rdas/{sSNVs,sIndels}/[sample_ID].rda.