Preferences

To display the Preferences window, click View>Preferences. Preferences are preserved across sessions. To override preferences during a session, use the track display pop-up menu. Each section on this page describes the options on a tab of the Preferences window: General, Tracks, Mutations, Charts, Alignments, Probes, Proxy, Advanced, and IonTorrent.

To restore default preferences or modify other default settings not listed here, see the Modify the prefs.properties file page.

General

Select to distinguish regions with zero values (white) from regions with missing data (gray). Clear (default) to display both regions in the same way (white). Affects only bar charts and scatter plots.
Select to display all tracks in a single panel. Clear (default) to display data tracks (e.g., expression data) in one panel and feature tracks (e.g., genes) in another.
Select (default) to show attributes and attribute values to the left of the data panel. Clear to hide the attributes. This option and View>Show Attribute Display have the same effect on attribute display.
Select to outline the boundaries of regions of interest in black. Clear (default) to leave them without black boundaries.
Zoom in on search results. When selected (default) the zoom level is automatically adjusted so that the target feature fills the view after a successful search. If not checked, the target feature of a search is centered in the view but the zoom level is unaffected.
Change this to change the resolution (in base pairs) at which the sequence track becomes visible.
Change this to define how large a flanking region (in base pairs) IGV will add before and after a feature locus when you zoom to a feature, or when you view gene/loci lists in multiple panels.
Click here to change the background color of the IGV display.
Use this to set a default font size for labeling tracks and features.

Tracks

Default track height for bar charts, scatter plots, and line plots.
Default track height for all other tracks.

Name of an attribute in the sample information file. IGV uses the corresponding attribute value as the track name.

Select to expand feature tracks by default. You may have to restart IGV for this to take effect.

Collapsed:

Expanded:

Select (default) to show the "expand/collapse" triangular icon on feature tracks.

Collapsed with the icon:                          Expanded with the icon:

                           

Select to normalize tracks containing coverage data in .tdf files that were created using igvtools.  This normalization option multiplies each value by [1,000,000 / (totalReadCount)]. 

  • This is only available for .tdf files created using igvtools builds dated 1/28/2010 or later.  Earlier versions of igvtools did not record the total read count.
  • This selection takes effect with new sessions loaded afterwards.

Mutations

Select to overlay mutation data on other tracks. more...
Name of an attribute column in the sample information file. IGV uses the corresponding attribute values to "link" mutation tracks with other tracks. more...
Select this to show mutation tracks that are not linked to other tracks, and therefore will not be seen if the overlay option is checked.  This option has no affect if the overlay option is not selected.

Select to color-code mutation data. To view and change the mutation coloring scheme, click the Choose Colors button. The Edit button next to Mutation in View>Color Legends also displays the same dialog. Alternatively, set default mutation coloring by modifying the prefs.properties file.

Mutation color codes are assigned dynamically. An example assignment chart is shown (Screenshot 2015.02.18).

Charts

Select to add a border at the top to the track.
Select to add a border at the bottom of the track.

Select (default) to color the top and bottom borders (if any). Clear to show the borders in black regardless of the track color. Tip: To change the track color, use the track display pop-up menu.

Select to label the track with its name, provided the track is at least 25 pixels high.
Select to label the y-axis with its data range.
Select (default) to allow charts (barchart, scatterplot, and lineplot) to automatically adjust the plot Y scale to the data range currently in view.  As the user pans and moves, this scaling continually adjusts.  Clear to turn autoscaling off.  There is an option in the popup menu to enable autoscaling for a single track.

Select (default) to show the range of the data.

Select to show all features in heatmaps.

The following figures illustrate these track display options.

  • Color borders selected (default):
  • All options selected:

 

Alignments

Sets the threshold at which IGV displays reads. Reads are visible only when IGV is zoomed in to display a number of bases less than or equal to this threshold.

Downsampling

IGV displays a specified number of randomly sampled alignments configured by the downsampling parameters instead of keeping all of them in memory. The coverage track, displaying total coverage at a region, is unaffected; that is, it always shows unsampled values. Default setting downsamples up to 100 per 50 nt window and paired reads are downsampled as a set.

  • Downsample reads: Deselect to turnoff downsampling.
  • Max read count: The maximum value that can be set is 100,000 reads per window. IGV uses reservoir sampling, so that all reads are kept if the read count is less than Max read count. If the read count is greater, the probability of any given read being sampled is equal to (Max read count) / (actual read count).
  • per window size (bases): Sampling is performed over windows, using the window size specified here.

Downsampled regions are marked by black rectangles spanning the downsampled region just under the coverage track as shown in the screenshot below. When zoomed out, the black rectangles may appear like a continuous black line.

Filter and Shading Options

For more information, see the Sequence Alignment/Map Format Specification.

  • Coverage allele-fraction threshold: Sets the mismatch threshold at which bases on an alignment coverage track are colored. The default is 0.2, i.e., if a nucleotide differs from the reference sequence in greater than 20% of reads, IGV colors the bar in the coverage bar chart in proportion to the read count of each base (ACGT). The threshold for an individual track can be changed from the pop-up menu.
  • Quality weight allele fraction: Deselect to disable quality weighting of the allele fraction when displaying single nucleotide mismatches in the coverage track for sequencing data. Prior to IGV v2.3.46, allele fractions automatically displayed quality-weighted fractions. The tooltip metrics reflect nonadjusted fractions. The numbers preceding + and - correspond to strand-specific counts, and sum to the total.
  • Filter duplicate reads: Clear to display alignments marked as duplicate reads. In DNA-Seq alignments these PCR or optical duplicates are often marked and filtered. In RNA-Seq alignments considerations differ.
  • Filter vendor failed reads: Clear to display reads that fail the vendor quality check.
  • Filter secondary alignments: Select to hide all secondary alignments for a read and display only the primary alignment. A read may map ambiguously to multiple locations, e.g. due to repeats. Only one of the multiple read alignments is considered primary, and this decision may be arbitrary. All other alignments have the secondary alignment flag. 
  • Filter supplementary alignments: Select to hide all supplementary alignments for a read and display only the representative alignment. A chimeric alignment that is represented as a set of linear alignments that do not have large overlaps typically has one linear alignment that is considered the representative alignment. Others are called supplementary and have a supplementary alignment flag.
  • Filter alignments by read group: Select to hide alignments that match the read groups listed in the filter file. The filter file is a text file that lists read groups, one per line.  This option means that IGV does not load the alignments associated with these read groups. Specify a URL or absolute file path to the file. Read groups are designated in the SAM format file header section under @RG.
  • Mapping quality threshold: Sets a threshold on alignment mapping quality. Only alignments with mapping quality greater than or equal to this threshold are shown.
  • Shade mismatched bases by quality: Select (default) to shade mismatched bases by quality, with lower quality being more transparent. A commonly used base quality metric is the Phred quality score, represented as Q, as detailed in Wikipedia

Phred quality scores are logarithmically linked to error probabilities with typical ranges between Q2 and Q63. For example, Q10–Q15 correspond to 10%–3% base call error probabilities (cutoff range recommended by Trimmomatic), Q20 to 1% error probability or 99% base call accuracy probability (conservative cutoff recommended by GATK), and Q60 corresponds to a one in a million error probability or 99.9999% base call accuracy probability. Differences in Q for the Sanger versus Solexa/Illumina GA platforms are graphed in this Wikipedia entry that shows diverging probabilities for scores less than Q13 for the different platforms. The same entry discusses Phred+33 versus Phred+64 systems of scoring, with the former being more prevalent for more recent platforms.

  • Flag insertions larger than: Select to flag reads containing insertions larger than the specified bases. An insertion within a read is denoted with a purple I () as detailed in Viewing Alignments. When this feature is activated, the I symbol is colored red for insertions larger than the size specified.
  • Show center line: Select so that, when zoomed in sufficiently, IGV displays a line at the center of the display. At higher resolutions, the center line becomes two lines that frame the aligned bases at the center of the display, as shown in the figure above.
  • Show coverage track: Select to display a coverage track for each alignment track. The coverage track is visible only when alignments are visible. It displays a gray bar chart showing the depth of the reads at each locus. If a nucleotide differs from the reference sequence in greater than 20% of quality-weighted reads, IGV colors the bar in proportion to the read count of each base (A, C, G, T). Modifying this option affects the display of subsequently loaded alignment tracks. Note, to change the threshold from the default 20%, see Coverage allele-freq threshold.
  • Show soft-clipped bases: Select to show the soft clipped sections of the read.
  • Flag unmapped pairs: Select to draw a red box around any paired alignment whose mate is not mapped.

Splice Junction Track Options

  • Show junction track: Select to display the splice junction track.
  • Min flanking width: The minimum amount of nucleotide coverage required on both sides of a junction for a read to be associated with the junction. This affects the coverage of displayed junctions, and the display of junctions covered only by reads with small flanking regions.
  • Min junction coverage:  The minimum number of reads associated with a junction required for the junction to be displayed.
Sets default size thresholds for color-coded flagging of paired end alignments. Only paired end alignments with insert sizes between these thresholds are flagged.  Select Compute to compute selected values from the actual size distribution of each library.

 

 

Probes

Select an option to determine how IGV places expression data on the genome:

  • Map probes to target loci: Use the probe ID to determine the probe locus and display data at that location. If that fails, map the probe ID to a gene, determine the gene locus, and display data at that location.
  • Map probes to genes: Map the probe ID to a gene, determine the gene locus, and display data at that location.

Modifying this option affects the display of subsequently loaded alignment tracks.

Proxy

Sets proxy parameters for connecting to the Internet.  IGV will use this to load hosted genomes and hosted data sets.
Select and enter values if a username and password is required for the proxy.
Clears all proxy settings.

Advanced

Select this option to enable a port on which IGV listens for commands and http requests. Enabling the port allows control of IGV from a web browser. more...

Select this option to edit URLs for the IGV data and genome servers. These settings are rarely changed. 

IGV caches each genome that it loads. On rare occasions, it may be necessary to clear the cached genome file to display an updated version of the genome. Click Clear Genome Cache to do this.

Genome Server URL is the URL for the genome server that populates the genome drop-down list.

Data Registry URL is the URL for the hosted data sets registry (populates File>Load from Server dialog).

Keep this selected to allow IGV to automatically check for updated genomes. Clear to disable this automatic check.

IGV 2.2, released December 18, 2012, and newer versions allow disabling anti-aliasing. This can significantly improve performance in some circumstances with running with X-Windows.

IGV 2.3.46, released March 2015 allows BLAT sequence searches of features, aligned reads, and selected regions of interest of up to 8 kb in length via right-click pop-up menu. Change the server hosting the genome against which BLAT searches. The default is the BLAT server hosted by UCSC's Genome Browser. Most UCSC derived genomes are supported, including human and mouse genomes.
This allows you to move your default IGV directory.

 

IonTorrent

Flow signal distribution chart options
Server settings