How to download allele frequency for all HUGO genes if I select all cancer cohorts in cBioPortal?
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Obtaining European allele frequencies for TopMed SNPs
written by 4galaxy77
-
Fetch HGNC id from gene symbol in python
written by gopi •
-
Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type)
written by erica.fary •
-
Using VEP to get gnomAD frequencies
written by brett.spurrier •
-
Converting TCGA/GDC IDs
written by krc3004 •
-
Allele frequency calculation
written by nkausthu •
-
Using Zagros & understanding its results
written by anu014
-
Plot minor allele frequency distribution in R?
written by dam4l
-
Ensembl Perl API - How to get genotype frequencies
written by entheologist33 •
-
Getting Population Specific Allele Frequency For Illumina Genotyping Data
written by yling1 •
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,
Thanks Maruthi. I have stopped using cBioPortal itself as I found TCGA's 'Firebrowse' more useful. They got an interactive API for getting data.