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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Is there a way to disable ClinVar for testing ? #459

Closed Tintest closed 1 year ago

Tintest commented 1 year ago

Hello,

I am working on a project for which I want to use Exomiser. For this, I want to qualify it on a true positive patient dataset from my laboratory, for which the diagnostic variants have been uploaded in ClinVar. I would like to test the performances of the tool without relying on the ClinVar data as this represents a confirmation bias.

I have commented in the application.properties file the exomiser.hg38.variant-white-list-path and exomiser.hg19.variant-white-list-path values, but the ClinVar data is still in the HTML report. Is there a way to completely disable ClinVar in Exomiser?

Regards.

damiansm commented 1 year ago

Hi,

This is a bit confusing but you have done the right thing by disabling it in the application.properties file. The data still displayed in the HTML report is just for user information then but does not contribute to the variant or overall scores. Basically if those two whitelist files are used in Exomiser, any variants found in those files get a max variant score of 1 regardless of the usual sources of variant score data: allele frequency, predicted pathogenicity etc.

Best wishes Damian

On Mon, Oct 24, 2022 at 3:13 AM Tintest @.***> wrote:

Hello,

I am working on a project for which I want to use Exomiser. For this, I want to qualify it on true positive patient data from my laboratory, for which the diagnostic variants have been upload in ClinVar. I would like to test the performances of the tool without relying on the ClinVar data as this represents a confirmation bias.

I have commented in the application.properties file the exomiser.hg38.variant-white-list-path and exomiser.hg19.variant-white-list-path values, but the ClinVar data is still in the HTML report. Is there a way to completely disable ClinVar in Exomiser?

Regards.

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Tintest commented 1 year ago

Hello,

Thank you for your prompt answer.

Regards.