Display B-allele frequencies in IGV WEB

[frank Musacchia]

Hello there,

I can correctly display a file like this containing BAF tracks and is named prova.igv in IGV Desktop App.

But when I open the same file with IGV-WEB I get the following error:

Unable to load track file baft.IGV - unknown file format

#type=GENE_EXPRESSION

#track graphtype=points name="BAF." color=0,0,255 altColor=255,0,0 maxHeightPixels=80:80:80 viewLimits=-1:1

Chr     Start   End     Features        values

1       10146   10147   1 10146 0.933333333333333

1       10229   10231   1 10229 0.5

1       10492   10492   1 10492 0.333333333333333

Do you have any reason for this? And in alternative what other format can I use to display B-allele frequencies in IGV-WEB app?

Thanks a lot

Francesco

[James Robinson]

The "IGV" format is not currently supported, as you discovered.   To suggest an alternative I need to know what you are trying to accomplish.   The file snippet you provide looks a lot like "bed" or "begraph", the choice would depend on how you want to view it.   If you zip and attach an example file with a screenshot I could make some suggestions.

Is there something special about "B-allele frequencies"?   

[Francesco Musacchia]

Hi James,

thanks for your reply.

BAF is an additional proof when inspecting CNVs in IGV.

I would need something  which could displayed decimal values as points.

Please find in attachment an example of a file with data and the corresponding screenshot in IGV.

How would you make it?

Best regards,

Francesco

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[James Robinson]

As there is only a single sample in this file the "igv" format is not needed, a simple bedgraph will suffice.  It is almost the same format, I converted yours with the following steps

(1) remove the "Features" column.      cut -f1,2,3,5 baft.IGV > tmp

(2) remove lines containing "NA" for value.     grep -v NA tmp > baft.bedgraph

(3) open baft.bedgraph in a plain text editor and remove #type=gene_expression line,  and leading # symbol in front of track line.

Load file to igv.org/app.    I've attached the converted file, and a screenshot below.   BTW if moving files to systems that have case-sensitive file names use of capitals for extensions might cause issues (e.g. .IGV instead of .igv).   I think most of our "igv" apps take care of this but some tools might not.

[Francesco Musacchia]

Dear James,

thanks for your kind help. I did try your .bedgraph on the website and it works. Nonetheless, it didn't on the system I am using. It shows lines instead of points (see attached pic). Anyway, as I have displayed, I do have an older version of IGV-WEB. I guess this is the reason, right? What do you think? I have contacted the system admin to update to the current version that should be 1.6.3

Francesco

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[James Robinson]

Try it at https://igv.org/app.   I do not recall when the "points" option was added.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAN4Ma--mo79xqXUDTfB8uhPh5T5jyca0k6Qk73H3g3prj%2BVY%3Dw%40mail.gmail.com.

[Francesco Musacchia]

Yes, I tried and it works. And after the update it works as well in our system. 

Many thanks 

Francesco 

Il giorno 8 nov 2021, alle ore 16:59, James Robinson <jrob...@broadinstitute.org> ha scritto:



Try it at https://igv.org/app.   I do not recall when the "points" option was added.

On Mon, Nov 8, 2021 at 5:52 AM Francesco Musacchia <francesco...@gmail.com> wrote:

Dear James,

thanks for your kind help. I did try your .bedgraph on the website and it works. Nonetheless, it didn't on the system I am using. It shows lines instead of points (see attached pic). Anyway, as I have displayed, I do have an older version of IGV-WEB. I guess this is the reason, right? What do you think? I have contacted the system admin to update to the current version that should be 1.6.3

Francesco

<Schermata 2021-11-08 alle 14.47.32.png>

Il giorno dom 7 nov 2021 alle ore 03:14 James Robinson <jrob...@broadinstitute.org> ha scritto:

As there is only a single sample in this file the "igv" format is not needed, a simple bedgraph will suffice.  It is almost the same format, I converted yours with the following steps

(1) remove the "Features" column.      cut -f1,2,3,5 baft.IGV > tmp

(2) remove lines containing "NA" for value.     grep -v NA tmp > baft.bedgraph

(3) open baft.bedgraph in a plain text editor and remove #type=gene_expression line,  and leading # symbol in front of track line.

Load file to igv.org/app.    I've attached the converted file, and a screenshot below.   BTW if moving files to systems that have case-sensitive file names use of capitals for extensions might cause issues (e.g. .IGV instead of .igv).   I think most of our "igv" apps take care of this but some tools might not.

<Screen Shot 2021-11-06 at 7.11.39 PM.png>

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[James Robinson]

OK great.   If the webapp is missing other features let us know,  the goal is to have as close to 100% compatibility with IGV desktop as is possible.   I've entered an issue to support the "igv" format, although not needed in this case, here:  https://github.com/igvteam/igv.js/issues/1415.

[Francesco Musacchia]

Thank you James, If I have other issues or I need features I will let you know.

Best,

Francesco

Il giorno lun 8 nov 2021 alle ore 18:52 James Robinson <jrob...@broadinstitute.org> ha scritto:

OK great.   If the webapp is missing other features let us know,  the goal is to have as close to 100% compatibility with IGV desktop as is possible.   I've entered an issue to support the "igv" format, although not needed in this case, here:  https://github.com/igvteam/igv.js/issues/1415.

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