BAM viewer that displays by insert

[mcrusch]

Is there a BAM viewer that allows you to display by insert rather than only by read?

Most BAM visualization tools treat each read separately. However, for paired-end data, it can be helpful to view each insert as its own entity. I would imagine each read being a rectangle, with another glyph that either bridges the gap (probably a line) or shows the overlap (differently shaded rectangle, maybe?).

Or, as a compromise, it could display each read as a separate entity, but highlight a read when you hover over its mate, or something like that.

I had thought this was possible in IGV, but couldn't figure it out with the version I was using (this was awhile ago, though). My google skills have come up short on this question.

Thanks,
Michael

[maubp]

Have you tried the paired stacked mode in Tablet? The two reads are placed on the same row, with a dashed line between them. Mouse over one will highlight the other as well.

http://bioinf.hutton.ac.uk/tablet/index.shtml

[mcrusch]

I had never even run across Tablet. It looks quite slick, and I see the two paired-end modes. This is great, thanks!

[maubp]

I had thought this was possible in IGV, but couldn't figure it out with the version I was using (this was awhile ago, though)

Have you tried the current IGV yet? I think version 2.0 (May 2011) or later should show paired reads.

[Richard Finney]

bambino: java bam view and snp detector

Check out bambino:

https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html

for standalone viewer.

online viewer with public sample data sets:

https://cgwb.nci.nih.gov/cgi-bin/bambino

example:
<a href="http://imgur.com/YI1KB"><img src="http://i.imgur.com/YI1KB.png" alt="" title="Hosted by imgur.com" /></a>