Bug?

[Maria Gallegos]

Hi, 

My students are using the Clinvar Short Variants evidence track to display the pathogenic and likely pathogenic mutations that map to their gene of interest. 

There seems to be a bug. When they filter for pathogenic (only) they get nothing (And I confirmed with BBS1)

We know pathogenic mutations exist because when everything is displayed there are a larger number of red variants than when only likely pathogenic are displayed. 

Compare the two images (Above is Likely pathogenic and Pathogenic. Below is All):

This makes me wary of any of the filtering capabilities. For example, when I filter for missense mutations am I really seeing all the missense mutations? I suppose I could go directly to the Clinvar database but it would be nice if this filtering mechanism worked because it could be cool and powerful. 

Maria

PS. This is using the 2013 Human Assembly

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[Matthew Speir]

Hello, Maria. 

Thank you for reporting this issue with the Clinvar SNV track. There was an issue with the filter configuration that we have now corrected. If you navigate to BBS1 and use the 'pathogenic' filter, you should see the results you expect.

If you have any further questions or run into other issues with the Genome Browser, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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