IGV SNP glyph question

Question

[mark.rose]

Hi All

I'm visualizing an alignment of Illumina paired end data in IGV. Some of the SNPs observed are rendered as glyphs consisting of a solid bar where as others appear as a bar with a gap in the middle. Looking at the alignment it appears that the gapped bar occurs where read1 and read2 do not agree but I am not positive of this. Does anyone know if this is correct, and, if not, what is the true explanation.

Thanks much

Mark

[finswimmer]

Hello mark,

could you please post a screenshot of IGV?

fin swimmer

[mark.rose]

This is with v 2.4.10 which has some advanced graphics for viewing paired read overlays

[GenoMax]

@mark please use the directions here: How to add images to a Biostars post

[mark.rose]

[mark.rose]

Dont know why its not visible in the post but if you right click either of these links the you can open the image

Ah, wait. Now its visible

[Ram]

Did you read my comment here? C: IGV SNP glyph question

[mark.rose]

Note the darker arrowhead of read 2's overlap at position 15

[mark.rose]

Both of the links I sent (imgur and cubupload) open when I right click on them but not within the post itself

[Ram]

I think you picked the wrong link. The link you used is part of cubeupload's HTML embed code. It's used in the <a href= part and not the <img src= part, (it is not a direct link to the image file, just to a webpage). If you see the How-to post, the direct link, highlighted in blue, stars with i.cubeupload. That link will work, not the one you used.

[Ram]

imgur works too, you just gotta use the direct link to the image (https://i.imgur.com/x77Z27m.png) and not the website URL from the browser address bar (https://imgur.com/a/ka2N8xB).

Answer 1

[finswimmer]

Looking at the alignment it appears that the gapped bar occurs where read1 and read2 do not agree but I am not positive of this.

You use the option "View as pairs". The region where you have this "gap" is the region where the read overlaps. The horizontal line isn't just where the SNPs are located.

fin swimmer

[mark.rose]

Not sure of your point. Yes, I am viewing them here as pairs. When I view them singly, they are solid bars, where the blue ones (in this case) are present only in one of the two overlapping reads. For other SNPs (viewed as pairs, not shown) that occur in overlapping regions but are called in both reads, the bar is solid.