VisCap.cfg

#VisCap configuration file for Linux users


interval_list_dir           <- "/path/to/dir/bed"  # directory where the interval file is stored 
#explorer_file               <- "C:\\Windows\\explorer.exe"
cov_file_pattern            <- "sample_interval_summary$"  # this is the extension of the coverage file from DepthOfCoverage
cov_field                   <- "_total_cvg" # field to be read from coverage file
interval_file_pattern       <- "interval_file.bed$" # interval filename
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

#Setting a path to data skips prompts. Set to FALSE for deployment.
dev_dir     <- FALSE