This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Pan-cancer dataset of GENIE control data download and sharing

Hi All,

The GDC has released genomic data for 44,756 cancer cases spanning 294 disease types from ⁦‪AACR‬⁩ Project GENIE. Who knows how to download Masked Annotated Somatic Mutations, Gene Level Copy Number Scores and Transcript Fusion data since they are controlled.

Thanks.

genie cancer maf cnv fusion
• 1,618 views • link
updated by ATpoint ATpoint • written by Shicheng Guo Shicheng Guo

1 answer

Data are restricted (as most data of human origin in public databases). The docs explain how to apply for access: https://gdc.cancer.gov/access-data/obtaining-access-controlled-data

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this
  • Appropriate genome reference for converting TCGA VCF files to MAF
    written by melissachua90 • melissachua90
    I have a directory of MAF files obtained from TCGA and I want to convert it to VCF format. Data source: https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-KIRP%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22files.data_category%22%2C%22value%22%3A%5B%22Simple%20Nucleotide%20Variation%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22maf%22%5D%7D%7D%5D%7D&searchTableTab=cases Reference: GRCh38.d1.vd1 Reference …
  • HT-seq CPTAC,RNA-seq
    written by Rob • Rob
    Hi friends I am trying to download HT-seq CPTAC RNA-seq for kidney and there is no HT-seq in the workflow section. Instead there is star-count. …
  • Matched tumor/normal RNASeq expression counts in TCGA
    written by ariel ariel
    I would like to download matched tumor/normal expression data from TCGA. I would also sample data like age, sex, race, etc. I looked at the …
  • TCGA germline and somatic snvs
    written by SUMIT • SUMIT
    I download the TCGA Masked SNVs using [link ][1] . TCGA website claims that > "Somatic MAFs (*somatic.maf), which are also known as Masked Somatic …
  • Meaning letters in TCGA sample barcode field
    written by sumitguptabt • sumitguptabt
    I have mapped the UUIDs to TCGA barcode using TCGAutils, however, I got some unexplained barcode such as UUID (Associated Barcode) 3d50d8ca-cabd-4129-80b9-ff1e84c190e5 (CPT0051690007) 54b12749-b94c-4284-a44b-ee890084141b (CPT0069370006) …
  • SSM Affected Cases in Cohort from DNA mutation of TCGA data portal
    written by Shicheng Guo Shicheng Guo
    Hi All, I am a little confused about how to understand the mutation information from mutation data of the TCGA data portal. Take [SMARCB1][1] as …
  • Downloading public RNA-seq raw read counts
    written by zizigolu zizigolu
    Hi, I am seeking RNA-seq raw read counts for **Oesophageal adenocarcinoma** Here I am not seeing any OESO https://www.synapse.org/#!Synapse:syn2812961 In this link I selected some …
  • Help convert GDC exploration url to API download?
    written by simplitia • simplitia
    Hi all, I have the search query from GDC https://portal.gdc.cancer.gov/exploration?cases_size=10000&facetTab=mutations&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.available_variation_data%22%2C%22value%22%3A%5B%22ssm%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-COAD%22%2C%22TCGA-READ%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22ssms.ssm_id%22%2C%22value%22%3A%5B%224fb37566-16d1-5697-9732-27c359828bc7%22%2C%22edd1ae2c-3ca9-52bd-a124-b09ed304fcc2%22%5D%7D%7D%5D%7D&format=tsv Is there a way to manipulate this perhaps through their api so that it points …
  • How to get the simple somatic mutation vcf file from GDC data portal?
    written by Vasu Vasu
    Hi, I wanted to download WXS somatic mutation file (VCF format) from GDC data portal [vcf file in gdc portal][1]. With the vcf file I …
  • GDC data only cancer sample without normal sample
    written by bharata1803 bharata1803
    Hello, I want to ask about data published in TCGA and now is hosted by GDC data portal. The link is this: [LINK][1]. After I …