Hi, I'd like to use FREEC without control to detect CNV in goat genome. I prepared my chromosome lenght file (goat_chr.len), my GC_content file, without mappability using bedtools on goat genome (example_GC_content.txt) and I prepared my config file: [general] chrLenFile = /illumina/runs/DNAPipeline/girgentana1/goat_chr.len ploidy = 2 GCcontentProfile = /illumina/runs/DNAPipeline/girgentana1/GC_girgentana_mod.cnp window = 50000 minExpectedGC = 0.30 maxExpectedGC = 0.70
mateFile = /illumina/runs/DNAPipeline/outRD.bam inputFormat = BAM mateOrientation = 0
I run FREEC and after reading the bam file It gives me the error: Your GC-content file /illumina/runs/DNAPipeline/girgentana1/GC_girgentana_mod.cnp is empty or is in a wrong format
Please use chomosome sequences (option "chrFiles") to recreate it!
Please I need some help to understand what I wrong. Any suggestion will be very appreciated. Greetings Marco