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LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis
GNU General Public License v3.0
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issue about Prepare HGMD-related data #104

Open zhangyuan5422 opened 2 weeks ago

zhangyuan5422 commented 2 weeks ago

I want to use AI-MAEEVEL to prioritize causal variants, but I cannot get the HGMD bgzip-compressed VCF file and HGMD Phenotype (hgmd_phenbase-*.dump.sql). Could you please give more details about how to do that? Thanks so much! image

SpicyChicken6 commented 2 weeks ago

Hello @zhangyuan5422 , if you are trying to run AIM code directly with HGMD data included, you might want to contact QIAGEN for purchasing the HGMD professional data license first, and they will provide the VCF and SQL data files needed here. We can't directly provide the HGMD data due to licensing issues. By default, the GitHub version of AIM run without HGMD data, at the cost of potentially lower accuracy.

However, you can also use our AIM web application at ai.marrvel.org to run your jobs by uploading your sample vcf and hpos, our AIM web application uses HGMD data for prediction so you don't need to purchase their data separately.