I am using VisCap (https://github.com/pughlab/VisCap/wiki) in order to conclude copy number variations by reading BAM files created from Ion Torrent next-generation sequencing on FFPE tumor samples. After successfully creating the required output from the GATK DepthOfCoverage tool and running VisCap using RTerm.exe I get the following error;
Error in make_matrix_from_cov_files(lane_dir, cov_file_pattern, cov_field) : object 'mat.cov' not found Execution halted
I've nearly tried everything from re-generating the reference genome index files (FAI, DICT) to re-running every individual analysis for each BAM going through the DepthOfCoverage tool, including the necessary update for the required R packages and sub-dependencies to make it run normally. I've contacted the corresponding author in the published paper, but never got an official reply, while the whole project seems abandoned (despite being published in a highly reputable journal). Therefore, I'm counting to anyone that might have used the software in the past or suspects anything that could solve the problem.