Configuration file VisCap.cfg

The config file contains the arguments that are needed to run VisCap:

interval_list_dir <- "/mnt/work1/users/pughlab/projects/EPIC/intervals" # this is a directory in which the interval file exists.

#explorer_file <- "C:\Windows\explorer.exe" # no need to modify this line

cov_file_pattern <- "sample_interval_summary$" # no need to modify this line

cov_field <- "_total_cvg" # no need to modify this line

interval_file_pattern <- "intervals.bed$" # the name of the interval file

ylimits <- c(-2, 2)

iqr_multiplier <- 3

threshold.min_exons <- 1

threshold.cnv_log2_cutoffs <- c(-0.55, 0.40)

iterative.calling.limit <- 0 #Set to 0 to iterate until all failed samples are removed

infer.batch.for.sub.out_dir <- TRUE #Set to FALSE to prompt users for output directory

clobber.output.directory <- FALSE #Set to FALSE to stop run when output directory already exists

interval_list_dir is the directory where you have stored your interval file. The input data has to generated by DepthOfCoverage and the 'cov_file_pattern' is the extension of the coverage files. The 'cov_field' is the field that is read from DepthOfCoverage files. You do not need to change these if you have the necessary files from DepthOfCoverage tool. And finally you need to put the name of the interval file or bed file in the 'interval_file_pattern". Do not change the rest of the config file.

Example:

interval_list_dir <- "/users/pughlab/projects/VisCap/intervals"

#explorer_file <- "C:\Windows\explorer.exe"

cov_file_pattern <- "sample_interval_summary$"

cov_field <- "_total_cvg"

interval_file_pattern <- "Five_panelGene_merged.bed$"

ylimits <- c(-2, 2)

iqr_multiplier <- 3

threshold.min_exons <- 1

threshold.cnv_log2_cutoffs <- c(-0.55, 0.40)

iterative.calling.limit <- 0 #Set to 0 to iterate until all failed samples are removed

infer.batch.for.sub.out_dir <- TRUE #Set to FALSE to prompt users for output directory

clobber.output.directory <- FALSE #Set to FALSE to stop run when output directory already exists