IGV: highlight both primary and supplementary alignments of a read

Question

[QVINTVS_FABIVS_MAXIMVS]

I'm using IGV and I grouped the alignments by supplementary tags Colored reads on the top panel are supplementary

How do I find the primary alignment of this read?

Answer 1

[Jim Robinson]

Hi, Zev is correct that IGV wasn't originally designed for SVs, however improvement in this area is a major thrust of development now. Specifically supplementary tags are recognized, and you can link supplementary alignments by right clicking the alignment menu and selecting "Link supplementary reads". If all reads are in view they will be linked similar to paired alignments by a line, or if they overlap you will see this with alpha transparency. Also, linked alignments that are inconsistent with respect to strand will be highlighted with color.

There are also features for 10X data, specifically if 10X barcodes are found in the data you will see 2 menu items, to link or by molecular ID. If phasing information is present they linked alignments will be grouped and colored by phase. This view is somewhat similar, by design, to the Loupe linked reads view.

This effort is still early, and I welcome feedback. The best place to do that is on our git forum, https://github.com/igvteam/igv/issues. There are topics open now specifically for PacBio and 10X, https://github.com/igvteam/igv/issues/277 and https://github.com/igvteam/igv/issues/275. I sometimes don't see postings here unless they are specifically called to my attention.

You can access the new features in the snapshot build, which requires Java 8, at http://software.broadinstitute.org/software/igv/download_snapshot

[QVINTVS_FABIVS_MAXIMVS]

Thanks Jim for all your hard work and dedication to IGV. Having this linked feature is going to make SV characterization so much easier

[Zev.Kronenberg]

Great (new?) feature. What version?

Answer 2

[Zev.Kronenberg]

The primary alignment and other chimeric alignments are listed in the "SA" optional field.

IGV wasn't specifically designed for viewing SVs. I don't know of a tool that lets you jump between the split reads.