Third Party Tool Integration
Image snapshots can be saved in Encapsulated Post Script (EPS) format using the EPSGraphics library. To enable this option, follow the steps below.
Once the library has been placed in the appropriate location, ".eps" will appear as an option under File > Save Image > File formats". Note that the image will not be created if you forget to restart IGV.
BEDTools is a fast, flexible suite of tools that can be used to compare large sets of genomic features. You can run BEDTools commands in IGV to compare features in loaded tracks and display the results as a new track. IGV povides access to the following BEDTools commands:
Using BEDTools with IGV
Before you can use the BEDTools feature in IGV, you must download and install BEDTools separately. (Note the known limitattion that BEDTools cannot be used on Windows). The user account running IGV must have permission to execute the BEDTools files. You also need to let IGV know where on your system to find BEDTools. Click on Tools>BEDTools>Set path to BEDTools... and enter the path to the installed BEDTools executable, e.g., /Applications/bedtools-2.17.0/bin/bedtools. (More detailed instructions for Mac users who do not know how to use the Terminal are here).
To see the list of available commands, click on Tools>BEDTools. The commands will be greyed out if you have not set the path.
When you click on a command, a dialog will appear. This is where you select the tracks to operate on, specify the name of the new track that will contain the results, and enter any other arguments to the BEDTools command. Most BEDTools commands take two inputs, so you will see two drop-down menus with the names of the tracks you have loaded into IGV. The following figure shows the dialog for the intersect command. See the BEDTools documentation for more information about each command.