Preferences

Change this to define how large a flanking region in base pairs. To specify the flanking region as a percentage of feature length, enter the percentage as a negative number. IGV adds the flank before and after a feature locus when you zoom to a feature, or when you view gene/loci lists in multiple panels.

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.

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. 

The default colors are shown below (Screenshot 2015.02.18).

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 (default) to show the range of the data.

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 (A, C, G, T). 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 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.

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.

UPDATE:  See here for new BLAT customization options as of release 2.10.3.