Running VisCap

For linux users:

1. Execute VisCap from the command-line using the Rscript program as following:

Rscript  VisCap.R   arg1=lane_dir   arg2=outputdir  arg3=VisCap.cfg

• lane_dir = path to directory where the DepthOfCoverage files are sitting
• output = path to directory where you want to output the results
• VisCap.cfg = Configuration file that you need to modify before running VisCap Example:

 Rscript /users/pughlab/bin/VisCap-master/VisCap.R \  /users/pughlab/DepthOfCoverage/output \ /users/pughlab/VisCap/output \
 /users/pughlab/VisCap/VisCap.cfg

It may be convenient to store this command as a .bat file containing the full path to VisCap and the path to the directory containing the interval list (i.e. bed) files used to run DepthOfCoverage and as input containing gene names for labeling of VisCap graphs. If running in non-interactive mode (mandatory for non-PCs that do not support the WinDialogue() command), the second argument must contain the desired output directory and the third argument must contain the path to the directory containing the DepthOfCoverage files.

2. If arguments are not provided, a dialogue box will appear (Windows only). Navigate to the lane directory that contains the sample subdirectories to be processed and click “OK”. These subdirectories should contain data files generated by GATK DepthOfCoverage.

3. A second dialogue box will prompt you for an output directory.

4. The analysis will go through multiple runs until all samples pass quality control. Each run will be stored as a separate folder (ex: “B1234_run1”, “B1234_run2”, etc.) that contains these files [link to output files page].