MAF File Validation Warning - Variant_Classification Mapping Issues

[Ji Hen Lau]

Hi,

 
I'm currently validating my MAF file for upload and have encountered a warning regarding the Variant_Classification column. The warning states:

"Given value for Variant_Classification column is not one of the expected values. This can result in mapping issues and subsequent missing features in the mutation view UI, such as missing COSMIC information."

Current Situation:
My MAF file contains variant classifications that appear to differ from the expected controlled vocabulary. Based on the documentation, I see the expected values include terms like:

• Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins
• Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site
• Translation_Start_Site, Nonstop_Mutation
• UTR and flanking region terms
• etc.

However, my data includes terms like:

• Start_Codon_Ins, Start_Codon_Del, Start_Codon_SNP, Stop_Codon_Del
• lincRNA

My Questions:

1. Should I remap my variant classifications to match the expected controlled vocabulary exactly?
2. Is there a comprehensive mapping guide available for converting common variant annotation terms to cBioPortal's expected format?
3. How critical is this warning? Will it significantly impact the functionality of my data in cBioPortal, particularly regarding mutation visualization and COSMIC annotations as stated?

Any guidance on best practices for handling this would be greatly appreciated.
Thank you for your time and support.

Best regards,
Ji Hen

[Prasanna Jagannathan]

Hi Ji Hen,

To see these variants in cBioPortal, add the below line to the Mutation data Meta file:

variant_classification_filter:

By leaving this field empty, all variants will be imported into the cBioPortal database and all variants will be visible on cBioPortal.

The full instructions are available in the link below:
https://docs.cbioportal.org/file-formats/#mutation-data

Please reply only to the <cbiop...@googlegroups.com> email.

thanks

Jag

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[Ji Hen Lau]

Hi Jag!

Yes, I already left the field empty as mentioned in the docs! But the issue I face is this warning:

"Given value for Variant_Classification column is not one of the expected values. This can result in mapping issues and subsequent missing features in the mutation view UI, such as missing COSMIC information."

And the value in my data that raises the warning is Start_Codon_Ins, Start_Codon_Del, Start_Codon_SNP, Stop_Codon_Del, lincRNA, which I believe is not listed in the docs.

So my question is:

1. Should I remap my variant classifications to match the expected controlled vocabulary exactly?
2. Is there a comprehensive mapping guide available for converting common variant annotation terms to cBioPortal's expected format?
3. How critical is this warning? Will it significantly impact the functionality of my data in cBioPortal, particularly regarding mutation visualization and COSMIC annotations as stated?

Regards,

Ji Hen

[Prasanna Jagannathan]

Hi Ji Hen

The easiest way is to remap the variant classifications to match the expected controlled vocabulary exactly. The tool vcf2maf is used as standard to match the cBioPortal expected format.

https://github.com/mskcc/vcf2maf

Please reply only to the <cbiop...@googlegroups.com> email.

thanks

Jag

[Ji Hen Lau]

Thanks for the clarification !