Mutation Mapper

[jillia...@gmail.com]

Is anyone else having issues with the mutation mapper. No matter how I input my data it is not creating a lollipop or even showing the variants in the table below. I have tried multiple input and genes. 

[Kelsey Zhu]

Hi Jillian, 

here are a few suggestions:

1. try load some sample data see if works from your end. 

2. view the required data format and check your input file for correct format.

3. share your input file for us to test.

Best!

Kelsey

On Fri, Sep 28, 2018 at 11:22 AM <jillia...@gmail.com> wrote:

Is anyone else having issues with the mutation mapper. No matter how I input my data it is not creating a lollipop or even showing the variants in the table below. I have tried multiple input and genes. 

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[Kelsey Zhu]

Hi Jillian,

The mutation mapper apparently was not happy with your chromosome locations. I loaded your test file with both Start_Postion and End_Position removed and fixed a typo (Protein_Change not Protien_Change), and got a lollipop plots (pease see attached). You could simply just have Hugo_Symbol and Protein_Change two columns. 

Best!

Kelsey

On Fri, Sep 28, 2018 at 11:53 AM Jillian Wise <jillia...@gmail.com> wrote:

Its still not working, here is a test file, however I also tried loading an entire MAF from another study and got nothing. Another colleague tried this input file and his own on a different computer. Also no results. 

[jillia...@gmail.com]

To clarify, i have used this succssefully last year, so I am wondering if the tool is down or a new update has rendered it no longer working?

 here is a test file, however I also tried loading an entire MAF from another study and got nothing. Another colleague tried this input file and one of his own on a different computer. Also no results. 

[Jillian Wise]

I now just entered only hugo symbol and protein change as you also mentioned, for some reason that worked versus giving it the start positions

I am so confused but at least I have output

Jillian

On Fri, Sep 28, 2018 at 7:05 PM Jillian Wise <jillia...@gmail.com> wrote:

I am still getting nothing...it now with the new input not even showing the HLA-A domain layout. Do you have the program installed locally versus the web version??

Bests

JIllian

[Jillian Wise]

I am still getting nothing...it now with the new input not even showing the HLA-A domain layout. Do you have the program installed locally versus the web version??

Bests

JIllian

[Ino de Bruijn]

Hi Jillian,

Sorry to hear you were having issues with the mutation mapper.

I dug a little deeper and the issue you are experiencing is because we made some changes recently. 

First off all, it annotates mutations on the fly if you give the following columns:

Chromosome Start_Position End_Position Reference_Allele Variant_Allele

Currently it only shows those mutations which affect the canonical transcript. For HLA-A that is ENST00000431930. According to the VEP annotator the list you sent us does not affect that transcript. I noticed that the mutations were in VCF format instead of MAF format which might throw the annotator off.

If you only have the columns:

Hugo_Symbol Protein_Change

It will use the provided annotations and show them displayed on the canonical transcript for HLA-A. This is why this *does* work in the current production version.

We're working on a new version of mutation mapper, which will display all transcripts for a given hugo symbol. It also won't override the annotations if they are provided by the user. That should get around issues like this. 

Best wishes,

Ino

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[Jill wise]

Thank you for the explanation, I should be able to use the current version more effectively now and I look forward to the new release

Bests

Jillian

Sent from my iPhone

[Ino de Bruijn]

Hi Jillian,

The new release for the mutation mapper is available now:

http://www.cbioportal.org/mutation_mapper.jsp

Please let us know if you run into any issues

Thanks,

Ino