CNVisualizer User Guide

Note

This is subject to change, mostly minor aesthetic changes.

Loading Tracks

In order to view the data, files must be loaded from one of the top two menu buttons. Choose which button based on where the file is being loaded from:

images/buttons.png
  1. File from a web server, must support Range Requests.
  2. File found locally on the computer.

And then you can input the relevant information, including

images/loadinput.png
  • URL or File, which is the data to be loaded. Track type is inferred off of the extension itself.
  • Name, which can be changed later (todo: ref)
  • Indexed, can NOT be used for local files. When used for URL files, it expects the indexed file to have the same URL, with the extra indexed extension (i.e. http://files.com/a.bam would be http://files.com/a.bam.bai).

Track configuration can be partially controlled with the gear icon, found to the right of each track:

images/control.png

Segment Track

Segment tracks have the following options available

CNV Called Track

CNV called tracks allow controlling

CNV Accumulated Track

Accumulation tracks allow choosing the segment tracks to include in the aggregation of data, as well as selecting an aggregation method. These can be seen as

images/accum.png
  1. Selected samples are marked with a ‘-‘ in front of them.
  2. Deselected samples are marked with a ‘+’ in front of them.
  3. Enabled aggregation method is marked with an ‘X’.
  4. Disabled aggregation method is let unmarked.