FAQ

Alignments

Q: I loaded a BAM file and don't see anything. What's wrong?

The most common cause for this is a mismatch in chromosome names between the BAM file and the IGV genome it is being viewed against.  The workaround is to create an alias file in 2-column tab-delimited format. To see how to create this alias file, see Creating a Chromosome Name Alias File in the IGV User Guide.

Q: I tried to compute coverage with igvtools and nothing was created. What's wrong?

Check the console output for error messages.  The most common causes for this are the two problems noted above for loading BAM files,  and attempting to compute coverage on an unsorted file.   

Genomes and Data Files

Q: How do I add [my favorite genome] to IGV?

Import the genome or contact the igv-help forum and request that it be added.

Q: I imported a genome annotation file and don't see the annotations. What's wrong?

The most common cause for this is a mismatch in the sequence (chromosome) names between the annotation file (e.g., GFF or BED) and FASTA files.  The workaround is to either rename the chromosome names in one of the files (usually the annotation file), or to create an alias file in 2-column tab-delimited format. To see how to create this alias file, see Creating a Chromosome Name Alias File in the IGV User Guide.

Q: How do I make a genome available to my colleagues on my server?

Follow the steps here to upload your genome to your server and configure it for sharing.

Q: How do I visualize [my favorite data type] in IGV?

Load your data into IGV. For help selecting the best file format, see File Formats. For tips on visualizing the data, see Viewing Data. If you still have questions, contact the igv-help forum.

Q: How do UCSC's genome release numbers correspond to those of other organizations, such as NCBI?

See the FAQ on the UCSC Genome Bioinformatics web site: http://genome.ucsc.edu/FAQ/FAQreleases#release1

Q: Does IGV assume log2(ratio) or absolute values for copy number?

IGV looks for the presence of negative numbers.  If it finds them, it assumes that the data is log2(tumor/normal).  If it does not find negative numbers, it assumes that the values are absolute, with 2 as the center.  These assumptions are used to set the heatmap legend; the legend can, however, be changed manually.

IGVTools

Q: I unzipped igvtools and double clicked the "igv.jar".  Nothing happened.

The igvtools jar is a command line program and must be run from a Linux or Mac terminal, or a Windows command prompt.  To start up a GUI interface for the program, launch igvtools from the IGV File menu, or use the script igvtools_gui,  igvtools_gui.bat,  or igvtools_gui.command depending on platform.  See the readme for more details. 

Q: When I try to run igvtools I get an error like the one below:

Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.

The scripts  (igvtools and igvtools.bat) include a memory flag on the startup line that needs to be reduced.  To fix this problem edit the igvtools file (igvtools.bat on Windows)  and reduce the amount of memory requested.   For example, to reduce the amount from the default 4GB to 2GB edit the startup line as follows

java -Xmx2g  -jar `dirname $0`/igvtools.jar $*

See the java documentation for more details. 

Q: I tried to sort/index a BAM file and it did not work.

IGVTools do not work with BAM files.  To sort or index BAM files use samtools.

General

Q: How do I export a sequence in which I am interested?

To export a sequence, first define the region using the Region of Interest tool.

After defining the region, click on the red bar to get a menu, and select Copy sequence.  You can then paste the sequence into a document.

Q: When I zoom into the sequence, why do I see little squares instead of the bases?

The squares appear when the sequence is unavailable. If you are using a genome stored on the IGV data server, you must be connected to the Internet to view the sequence.

Q: How do I clear IGV from my Java cache so that I can update my IGV?

On Windows:

1) Delete the icon from your desktop, if it was there to begin with.
2) Open Control Panel > Java and select the General tab.
3) In the Temporary Internet Files section, click View.
4) Select Applications from the drop-down menu and delete any IGV applications you see.
5) Select Resources from the drop-down menu and delete any IGV entries you find.
6) You may also need to clear your internet browser cache.
7) Go to http://broadinstitute.org/igv and launch IGV.

On Macintosh:
1) Delete the icon from your desktop, if it was there to begin with.
2) Open the Java control panel in System Preferences and open the General tab.
3) Click View... under the heading Temporary Internet Files.
4) Select Applications from the drop-down menu and delete any IGV applications you see.
5) Select Resources from the drop-down menu and delete any IGV entries you find.
6) Click Close.
7) Click OK in the Java control panel.
8) You may also need to clear your internet browser cache.
9) Go to http://broadinstitute.org/igv and launch IGV.

Q: How do I clear IGV's genome cache?

A) View>Preferences>Advanced>Clear Genome Cache
or
B) Delete the contents of the <igv home>/genomes directory

Q: A gene locus often produces several splicing isoforms, so how do I show different splicing isoforms for a single gene locus in IGV?

Right-click on the track and select Expand Track, or click the triangle icon () on the left-hand side of the track.  This displays overlapping features in separate rows so that separate isoforms are visible.

Q. When I launch IGV with the 2GB or 10GB options, I get an error that says, "Could not create the Virtual Machine."   I have plenty of memory on my computer so why is this happening?  

You need both a 64-bit OS and a 64-bit version of Java.  On many computers, 32-bit Java is installed by default, even if the OS is 64-bit.

SNPViewer Users

Q: Can I use an array list to display selected tracks in IGV?

Yes. See Sorting and Filtering by Track List.

Proxy

There is a known issue when proxies must be used with a new installation of IGV. When you are behind a firewall launching IGV for the first time, IGV might refuse to launch with an error that the genome server cannot be contacted.  If this occurs, the workaround is to manually place a genome in the IGV genome cache directory by performing the following steps:

1. Download the hg18.genome file from 

  http://www.broadinstitute.org/igvdata/genomes/hg18.genome

2.  Save the above file to the following directory,  creating it if needed.

      <user home>/igv/genomes    (Recent IGV versions, 2.1 and higher)

      <user home>/.igv/genomes   (2.0 and older, for Macs only -- note the dot before igv)

After starting up you can set your proxy settings in the preferences window after starting up (menu View > Preferences > Proxy tab).