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Visualize sequence read alignment data (BAM or SAM) on IGV using this quick-start tutorial. The Integrative Genomics Viewer is a non-GATK tool developed at the Broad Institute that allows for interactive exploration of large genomic datasets.
human_g1k_v37_decoy.fastathat corresponds to the
Human (1kg, b37+decoy)reference hosted by IGV.
To view aligned reads using the Integrative Genomics Viewer (IGV), the SAM or BAM file must be coordinate-sorted and indexed.
Human (1kg, b37+decoy).
6491_snippet.bam. IGV automatically uses the corresponding
6491_snippet.baiindex in the same folder.
10:96,867,400-96,869,400into the textbox at the top and press Go. A 2 kbp region of chromosome 10 comes into view as shown in the screenshot above.
Alongside read data, IGV automatically generates a coverage track that sums the depth of reads for each genomic position.
H0164ALXX140820:2:2107:7323:30703into the read name textbox and press OK. IGV will highlight two reads corresponding to this query name in bold red.
Because IGV holds in memory a limited set of data overlapping with the genomic interval in view (this is what makes IGV fast), the select by name feature also applies only to the data that you call into view. For example, we know this read has a secondary alignment on contig hs37d5 (
If you jump to this new region, is the read also highlighted in red?
If you find IGV sluggish, download a Java Web Start
jnlp version of IGV that allows more memory. The highest memory setting as of this writing is 10 GB (RAM) for machines with 64-bit Java. For the tutorial example data, the typical 2 GB allocation is sufficient.
jnlpversion of IGV, you may need to adjust your system's Java Control Panel settings, e.g. enable Java content in the browser. Also, when first opening the
jnlp, overcome Mac OS X's gatekeeper function by right-clicking the saved
jnlpand selecting Open with Java Web Start.
To change display settings, check out either the Alignment Preferences panel or the Alignment track Pop-up menu. For persistent changes to your IGV display settings, use the Preferences panel. For track-by-track changes, use the Pop-up menus.
Default Alignment Preferences settings are tuned to genomic sequence libraries. Go to View>Preferences and make sure the settings under the Alignments tab allows you to view reads of interest, e.g. duplicate reads.
prefs.propertiesfile within your system's
igvfolder. IGV automatically generates a new
prefs.propertiesfile with default settings. See [IGV's user guide] for details.
After loading data, adjust viewing modes specific to track type by right-clicking on a track to pop up a menu of options. For alignment tracks, these options are described here.