View as pairs not functioning.

[P SM]

I am running IGV v 2.3.32 (37) with 12 GB of ram allotted to Java on a Win7 machine.

I find the "view as pairs" option very useful when perusing .bam files of paired Illumina reads mapped to a reference genome. However sometimes it mysteriously fails to function. That is, I can successfully click the option "View as pairs" in the context menu by right-clicking in the main window displaying the reads. The option then shows a check next to it. But the reads are not grouped as pairs, nor do they show a line connecting pairs.

The .bam file does apparently contain the pairing information because windows pop up during mouse-overs telling me about the read and its successfully mapped pair and the insert distance between them.

Any tips?

I have tried downloading the newest version of IGV and running it and using a webstart version -- same result.
I have tried deleting the igv.log and prefs,properties files from the igv directory. No joy.
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Phillip

[Jim Robinson]

Hi,

Could you send us a sample bam file that exhibits the problem?   Just extract a small region that show the problem.   It will need to be large enough to contain both ends of a pair.   I don't want to speculate too much without a file, but  just because mate-pair information is available in the popup does not necessarily mean that the mate is really in the file.   

Jim

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