VisCap 'mat.cov' not found error in R

Question

[ceruleanivy]

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.

Answer 1

[hns]

Hi Ceruleanivy,

You just need to change the cov_file_pattern to reflect the cov file pattern that you have.

Thank you.

[luckyluke95]

Dear Ceruleanivy and hns

Are you still using Viscap ? I just have some questions but the Github forum seems to be off...

Thanks in advance

L.

Answer 2

[nkausthu]

I have the same issue. It would be really great if someone can comment on this

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

as.Date, as.Date.numeric

character(0) Error in make_matrix_from_cov_files(lane_dir, cov_file_pattern, cov_field) : object 'mat.cov' not found Execution halted