Viewing AlignmentsThis page introduces viewing alignment data and associated tracks in the following sections: Related topics on other pages cover more detailed topics:
File FormatsAligned reads from sequencing can be loaded into IGV in the BAM format, SAM format, or CRAM format. Both BAM and SAM files are described on the Samtools project page http://www.htslib.org and in the 2014 article titled Sequence Alignment/Map Format Specification by the SAM/BAM Format Specification Working Group. IGV requires that BAM and CRAM files have an associated index file.
If you receive a .bam file from a sequencing facility, you will usually also get the corresponding index file. If you need to create the index yourself, there are multiple tools available for indexing BAM files, including igvtools, the samtools package, and the Picard.SortSam module in GenePattern. Tracks
Loading an alignment file creates up to 3 associated tracks:
By default the Alignment and Coverage tracks are initially displayed. This setting can be altered from the Alignments tab of the Preferences window. Also, showing or hiding individual tracks can be controlled with track popup menus.
Note: If hiding the Alignment track by default you might also consider the setting to create all tracks in a single panel. This is in the General tab of the Preferences window.
The Coverage and Alignment tracks are described below. The Splice Junction Track is covered on a separate page.
Coverage TrackBy default IGV dynamically calculates and displays the default coverage track for an alignment file. When IGV is zoomed to the alignment read visibility threshold (by default, 30 KB), the coverage track displays the depth of the reads displayed at each locus as a gray bar chart. 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).
View count details by hovering the mouse over a coverage bar. Copy the count details to your computer's clipboard from the right-click menu. Pre-computed Coverage DataThe dynamically calculated coverage data can be augmented by loading pre-computed coverage data from a file. When this option is used the track displays coverage at all zoom levels including at the whole genome and chromosome view. To generate the extended coverage data file ending in TDF extension, use igvtools. The resulting file can be associated with the alignment track by file naming convention or loaded independently from the track popup-menu.
Visibility Range Threshold and DownsamplingIGV reduces memory usage in the following two ways to improve performance of viewing alignments.
You can adjust the above settings in the Alignment Preferences panel. For example, for lower coverage data, you can provide a larger visibility range threshold. Or for deep coverage, you might want to provide a smaller visibility range threshold and adjust the downsampling to show more reads. Downsampled reads areas are marked with a black rectangle just under the coverage track. The coverage track represents coverage for all the reads. In the example shown, the downsampled regions are marked by seven black rectangles just under the coverage track.
Alignment TrackThis section gives an overview of the alignment track. For options available from the alignment track menu, including grouping, sorting and coloring options, see the alignments section of the pop-up menu page.
Detecting Structural VariantsIGV uses color and other visual markers to highlight potential genetic alterations in reads against a reference sequence. Genetic alternations include single nucleotide variations, structural variations, and aneuploidy. Structural variations include insertions, deletions, inversions, tandem duplications, translocations, and other more complex rearrangements. Interpretation of some of these variations are discussed briefy in this section and the next. Interpreting Color by Insert Size and Interpreting Color by Pair Orientation give more detailed explaination of read colors. An additional factor to take into consideration when judging potential genetic alterations is quality of reads and quality of mapping. IGV uses transparency to indicate quality.
Colors and transparency are used at two levels within alignments: (1) for mapped reads, and (2) for individual bases within reads.
Color and Transparency for Individual basesBy default, read bases that match the reference are displayed in gray. Read bases that do not match are color coded, and insertions and deletions within reads relative to the reference are marked. Insertions are indicated by a purple I (
Transparency for Mapped ReadsNote that alignments that are displayed with light gray borders and transparent or white fill, as shown in the screenshot, have a mapping quality equal to zero. Interpretation of this mapping quality depends on the mapping aligner as some commonly used aligners use this convention to mark a read with multiple alignments. In such a case, the read also maps to another location with equally good placement. It is also possible the read could not be uniquely placed but the other placements do not necessarily give equally good quality hits. Insertions
In a gapped alignment, IGV indicates insertions with respect to the reference with a purple I (
![]() DeletionsIn a gapped read, IGV indicates deletions with respect to the reference with a black bar. Coloring and Sorting AlignmentsUsers can also specifiy color and also sort reads by various options, including start location, strand, nucleotide, mapping quality, sample tag, or read group tag. For a description of all user-specified color and sort options, see the alignment track pop-up menu. For example, to sort alignments:
Sorting rearranges rows so that alignments that intersect the center of the display appear in the order specified. This can cause the alignment layout away from the center line to appear sparse. To restore the layout to an optimally packed configuration, select Re-pack alignments from the pop-up menu. Repeat the most recent sort with hotkey ctrl-s. Paired-End AlignmentsIGV provides several features for working with paired-end alignments. This section covers viewing reads as pairs, coloring of mapped paired reads, and the split-screen view. Interpretation of colors is discussed briefy here and in more detail in Interpreting Color by Insert Size and Interpreting Color by Pair Orientation. View As PairsBy default, IGV displays reads individually because they pack compactly. Select View as pairs from the right-click menu to display pairs together with a line joining the ends as shown in the image below. The hover element details (2) are also displayed either for a single read in normal view (left) or for a pair of reads in paired reads view (right).
Coloring of Mapped Paired ReadsIGV colors paired-end alignments in two ways.
Split Screen ViewSplit screen views can be invoked on-the-fly from paired-end alignment tracks. Right-click over an alignment and select View mate region in split screen from the drop-down list. If the alignment clicked over does not have a mapped mate this option will be grayed out. You can select this option for mutliple alignments and view multiple panels side by side.
To return to a normal single screen view, right-click on the locus name at the top of the panel you wish to keep and select Switch to standard view. Alternatively, double-click the locus name.
You can control the view of each panel independently. Pan by click-dragging in the panel; double-click to zoom in and alt-click to zoom out.
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