Query TCGA projects for variant presence
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20 months ago

Hi, I have a set of variants of which i want to know whether they are present is a set of (or even all) TCGA studies using an api or downloading files for a local query. It would also be helpful to get the cancer type associated with the found variant. Also the variants are only small indels & snps. The GDC website provides the exact function required for my project, but from what I can tell this is not possible using their api. I have already been searching for a while, since there are multiple ways to access TGCA data. But the cBioPortal api does neither get it done, nor am I 'authorised' to download any .vcf files from the GDC Legacy archive I really hope someone has an idea help me!

TCGA gene • 320 views
Entering edit mode

I don't understand your comment about "but from what I can tell this is not possible using their api". The entire GDC portal and all visualization tools are supported by the API. You might want to send an email to GDC help desk.


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