Loading a Genome

Genomes are selected from the genome drop-down list on the upper-left of the IGV window.  Intially, this list contains a single item, Human hg18 or Human hg19, depending on the version of IGV.  To add other genomes to the list, see the sections below on "Selecting a Hosted Genome" and "Loading Other Genomes".

• When you switch genomes, all data that is currently loaded in the browser is cleared, starting a new session (as if you had selected File>New Session).
• The genome selected when IGV exits is automatically selected when IGV restarts.

Selecting a Hosted Genome

IGV provides a number of hosted genomes.  If the genome you want is not in the drop-down list, either click on the More... entry at the bottom of the list, or select Genomes>Select Hosted Genome from the menu. This will bring up a list of all the hosted genomes, listed in alphabetical order. Scroll down to find the one you want, or use the 'Filter' to narrow down the list.

• Select the genome you would like to add to the IGV genomes menu, and click 'OK'. A new entry will be inserted in the drop-down list (in alphabetical order), and the display will switch to this genome.

• Checking the 'Download sequence' box will also download a FASTA file of the whole genome sequence, along with an FAI. index file.
  • The sequence will be downloaded into the folder <user_home>/igv/genomes/seq.
  • All available genomes are listed, even those that have already been loaded into the IGV drop-down list. This is in case you want to now download the sequence for a genome already in the menu.
  • Note that a downloadable FASTA file is not available for all hosted genomes. A notice will pop up if you try to download a sequence that is not available.
  • See here for information on downloading and configuring genome files for use with IGV without an internet connection.

Loading Other Genomes

If you have the .FASTA file for your reference genome sequence, it can be loaded by clicking on Genomes > Load Genome from File or Genomes > Load Genome from URL. In this case, the gene annotations will not be loaded automatically, but if you have the gene annotation file, it can be loaded like any other data file via the Files > Load from menus. To automatically load gene annotations, as well as an optional cytoband file, you can create a genome JSON file as described below. 

FASTA files can be plain text or block gzipped, and must be indexed with a .fai as defined by the Samtools suite (www.htslib.org). If the file is plain text (not block gzipped) and not indexed, IGV will attempt to index it.  IGV remembers the location of the FASTA file and the file will appear in the drop-down list until it is removed as described below.

Removing a Genome

To remove a genome from the IGV menu:

• Select Genomes>Remove Genomes.
• Select the genomes you want to remove and click Remove. Click Save to complete.
• Note that you cannot remove the genome that is currently used.

Creating a Genome JSON File 

In special cases it might be desirable to create a genome JSON file to define the reference. This option enables additional files to be associated with the FASTA reference sequence file, such as annotation track files. The genome JSON format is described in the IGV github wiki. The file name should have a ".json" extension. Once created it can be loaded from the Genomes menu. (This replaces the old .genome file, which has been deprecated).