how to visualize split reads in igv

[Nasir Amra]

Hello,

    I've done a lot of googling on this issue , but did not get a clear process for how to do so simple visualization of split reads in IGV (2.10). I hope detailing what I've done so far and my thought processes would help someone to answer my question.

I have a bam file with ALK-EML4 split reads which I've setup a multi view configuration in igv ( see image attached). I've managed to get the read name for one of the split reads (primary alignment to ALK and supplementary alignment  to EML4) by going through the .sam file to copy the read name to the "select read name..."popup menu item causing that read to be colored. I expected that same read would have an alignment under the EML4 pile up and that it would also be colored. However, I don't see that. Am I missing something here ( this area is all new to me)?

It would also be helpful if one can click on a read and have it selected instead of typing in a long read name ( or in my case copying and pasting from sam file). 

I tried clicking on "link supplementary" popup menu item , but all that did was move the read in the pileup to somewhere below. I don't understand what this menu item does.

If anyone can point me to any process to do this simple thing , I would be grateful.

Cheers,

Nasir

[James Robinson]

Hi, you cannot view split reads across multiple locus views.   "Link supplementary" will link split alignments together as long as all are visible in the same view.  This is useful for many genomic SVs, but is not useful for fusion genes or other long range rearrangments.  We do not have a solution for that case yet, in any event "link supplementary" will not do anything across view boundaries in a multi-view configuration.

If you command-click on a read it will highlight all alignments with that read name, even across multiview boundaries.

[Nasir Amra]

Thanks for clarifying this limitation of IGV. I did try the command-click in a multi view setting on a read with a primary alignment in the left view ( ALK gene) and although the read details indicated that there was a supplementary alignment in the right view ( EML4) , I don't see the same colored read (and therefore the same read name)_ as the select read on the left view. Am I missing something here?

Cheers,

Nasir

[James Robinson]

No,  you are not missing something AFAIK,  all alignments with that read name should be highlighted.   This is illustrated in the screenshot below, the alignment on the right is marked "supplementary"

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[Nasir Amra]

I got the same effect after turning off read downsampling in preferences. I was also able to sort by read name for each view in the multi-view.

Thank you.

Cheers,

Nasir

Sent from my iPhone

On Jun 22, 2021, at 10:21 PM, James Robinson <jrob...@broadinstitute.org> wrote:



No,  you are not missing something AFAIK,  all alignments with that read name should be highlighted.   This is illustrated in the screenshot below, the alignment on the right is marked "supplementary"

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpvcKPYW2s0y1_7ncNBj7O%3DqztC%3DBbxRdABQcu4ALMbjug%40mail.gmail.com.