How to download allele frequency for all HUGO genes if I select all cancer cohorts in cBioPortal?

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8.7 years ago

anu014 ▴ 190

I am trying to get allele frequencies for all gene symbols present in HGNC for all Cancer types present on TCGA. In Web-API, there is no way to get allele frequency directly as it's shown in cBioPortal's query. So I tried to write a perl script to download 'mutation table' for each cancer type, but I couldn't get it. I even tried to download open access MAFs, but I couldn't get the allele frequency column in it. Is there any way to download the mutation data which includes allele frequency with it?

Regards,
Anupriya Verma

allele gene • 2.2k views

ADD COMMENT • link updated 18 months ago by Ram 43k • written 8.7 years ago by anu014 ▴ 190

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Hi, I am assuming by now you would have sorted your issue. I am sorry if the below link does not answer your query. Just thought it might give you more info which might be useful.

https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format

Best wishes,

ADD REPLY • link 8.6 years ago by maruthi ▴ 10

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Thanks Maruthi. I have stopped using cBioPortal itself as I found TCGA's 'Firebrowse' more useful. They got an interactive API for getting data.

ADD REPLY • link 7.6 years ago by anu014 ▴ 190

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