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Combines variants and CNAs to clonal evolution
getStories(variants, cnvs, timeSeries, normals, genome,
cloneDistanceCut = -qnorm(0.01), Rdirectory, plotDirectory, cpus = 1,
forceRedo = F, manualStoryMerge = F, correctReferenceBias = T,
rareGermline = T, maxStories = 3000)variants: The variants.
cnvs: The copy number calls.
names list of vectors: samples to be analysed together, named by individual.
named boolean vector: which sameples (names of vector) are normal.
character: the genome.
character: The save directory.
character: the directory to plot to.
integer: maximum number of parallel processes. Default 1.
boolen: if redoing calculations even if saved data is available. Default FALSE.
This function calls VEP on the output from outputSomaticVariants. For this, VEP needs to be callable by system('vep').