postAnalyseVEP

named list with Rdirectory and plotDirectory.

outputDirectories

inputFiles

character: such as 'hg19', 'hg38' or 'mm10'

genome

integer. maximum number of parallel threads.

cpus

character: path to COSMIC directory. (optional)

cosmicDirectory

boolean: if TRUE, previously saved data is ignored and overwritten.

forceRedo

Runs VEP on a R and plot directory that superFreq has been run on.

SuperFreq analyses SNVs and CNAs of multiple cancer exomes, sharing
all information across samples and mutation types. The inputs are the bam-files
and a preliminary SNV calling in .vcf format. SuperFreq filters and annotates
the SNVs, calls CNAs and tracks clones over samples from the same individual.
A matched normal improves results, but is not necessary. SuperFreq requireas at
least two (preferably 5-10 or more) reference normal samples that do not have to
be related to the studied cancer samples, but must be from the same sequencing
platform and capture. These are used to improve results through variance of read
depth and requrring false SNVs amongst other things. SuperFreq produces ample
output in terms of plots and spread sheets, both for identifying properties of
the cancer samples and for quality control.

postAnalyseVEP: Runs VEP on a R and plot directory that superFreq has been run on.

Description

Usage

Arguments

Details