Marking low VAF/low confidence mutations

[Thomas Pauli]

Hi everyone,

I have low_vaf mutations (<0.05) for some of the patients in my study which I would like to display alongside other mutations. However, I would like to add something like a "warning label" to these mutations. Do you have a good idea how I could do this? Is there a way to change the color of certain mutations, or a way to add custom symbols to one of the columns? 

I would prefer a simple way to mark samples or certain mutations with a color or a symbol. If that isn't supported, I thought of marking the low vaf mutations by adding them as a second sample and change the color of the sample number (see image below). However, I only seem to be able to do this, by changing the SAMPLE_TYPE to either 'Metastatis' or 'Recurred'. However, doing so will also add the SAMPLE_TYPE to the sample name and I want to avoid this. Is there a way to change the sample color in a different way, add a custom sample type, or keep the color and remove the Metastasis next to the sample name somehow?

Best wishes,

Thomas

[Benjamin Gross]

Hi Thomas,

If you put samples/variants in a separate molecular profile with the genetic_alteration_type “MUTATION_UNCALLED”, the sample number will be rendered with some translucency in the Mutation table on the row with the variant having low vaf.  An example is found at the following link for sample-1 - TET2:

https://www.cbioportal.org/patient?studyId=glioma_msk_2018&caseId=IM-GBM-1

You can see what the data file looks like here (look for meta_mutations_uncalled.txt):

https://github.com/cBioPortal/datahub/tree/master/public/glioma_msk_2018

Hope this helps.

-Benjamin

<Bildschirmfoto 2023-11-06 um 15.41.49.png>

Best wishes,

Thomas

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<Bildschirmfoto 2023-11-06 um 15.41.49.png>

[Thomas Pauli]

Hi Benjamin,

thank you so much for your suggestion. I think it's better to assign the variants to the same sample, so in principle this is what I was looking for. However, I think it's still not conspicuous enough. Another possibility I could think of would be to set the gene name or the row background to a different color or opacity, but I also don't know whether this is possible. Maybe you have (or someone else has) a good idea. 

I also know I could add a column via namespaces, but here I think it won't be visible enough as well.

Thomas

[Benjamin Gross]

Setting a different color background or opacity would require code changes.  As you suggest, adding a new column via namespaces to indicate low vaf status would work too and does not require code changes, but because the column would be positioned on the right, you would have to go through the process of hiding unnecessary columns to move this column into a prominent position.  Other cBioPortal team members may have better ideas.

Best,

Benjamin

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