INNER CODE UNIT · R
sambamba
igordot/genomics · scripts-bigpurple/cnvs-wgs-freec.sh:207
sambamba = /gpfs/data/igorlab/software/sambamba/sambamba-0.7.0
# file with chromosome lengths (fa.fai accepted starting from v9.3)
chrLenFile = $chr_len_file
# path to the directory with chromosomes fasta files
# necessary to calculate a GC-content profile if a control dataset and GC-content profile are not available
chrFiles = $chr_files_dir
# information about mappable positions (GEM output)
gemMappabilityFile = $gem
# use a mappability profile to correct read counts (provided with gemMappabilityFile)
uniqueMatch = TRUE
# genome ploidy
# you can set different values and Control-FREEC will select the one that explains most observed CNAs
ploidy = 2