Third Party Tool Integration

EPSGraphics

Image snapshots can be saved in Encapsulated Post Script (EPS) format using the EPSGraphics library. To enable this option, follow the steps below.

  • Download the library from the Abeel web site
  • Place the jar file in <igv home directory>/plugins. This directory may need to be created.
  • Restart IGV, if it was running.

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

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:

  • intersect: Identifies regions with overlapping features in two tracks. Exons are treated as separate features if the "-split" flag is included (default).
  • subtract: Removes regions in one track from another. For example, if you have a track of features and want to find all regions NOT in a gene, you can subtract the gene track from the feature track.
  • closest: For each feature in the first track, finds the closest matching feature in the second track. This may be an overlapping feature.
  • window: Similar to intersect, window searches for overlapping features. However, window adds a specified number (e.g.1000) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are near (e.g. within 1000 bp of) features in A to be detected.
  • coverage: Calculates the coverage of track A by track B.
  • multiintersect: Calculates regions where all of any number of provided tracks intersect.
Known Limitations
  • IGV does not currently support BEDTools integration on Windows. While BEDTools itself can be compiled and run under cygwin, IGV will not be able to interface with it.
Using BEDTools with IGV

Before you can use the BEDTools feature in IGV, you must download and build BEDTools separately, as described on their web site. 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.

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.