Displaying paired-end reads with "View as pairs"

[Ryan Golhar]

HI - I'm trying to use the "View as pairs" option to see how my forward/reverse reads are related to each other.  I noticed that IGV draws the connecting line connected to one read but not to a read on the other end.  At first I thought this was because the read wasn't paired properly, however I've come to see its because IGV draws the other read on the a different line per se so that the connecting line cannot physically connect the two.  Is there a way to get IGV to draw both reads together on the same line such that the connecting line between them actually shows them as connect?

[Jim Robinson]

Ryan, the way you describe it (both reads on the same line) is the way it is supposed to work, and is the way it works for the files I have (see screenshot).   It could be an IGV bug but I need to be able to reproduce it.  Could you extract a small region from your BAM to include the problematic reads and send the file to us at igv-...@broadinstitute.org?  

-- Jim