Access to mutation data

[Jason White]

Hello,

I’m trying to download the mutation data from this link: https://github.com/cBioPortal/datahub/blob/master/public/breast_ink4_msk_2021/data_mutations.txt but when I do, there’s no data. There’s a link to Git LFS but I’m not familiar with this tool, nor do I know how to use it if that is what is required to access this data set. 

Can you provide with instructions on how to download this data?

Thanks,

Jason

 

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[Ramya Madupuri]

Hi Jason, 

There are two ways to access the data. The instructions are available in the Datahub Readme here: https://github.com/cBioPortal/datahub/blob/master/README.md#how-to-download-data.

Option 1: Download the study Zip
You can download the study package directly from the cBioPortal Datasets or the Study page. The Zip contains the actual staging files, including the mutation data.

Option 2: Use Git LFS

1. Install Git LFS
2. Run:
git lfs install --skip-repo --skip-smudge
git clone https://github.com/cBioPortal/datahub.git
cd datahub
git lfs install --local --skip-smudge

3. Download the files for the specific study:
git -c lfs.fetchexclude="" lfs pull -I public/breast_ink4_msk_2021

Let us know if you run into any issues or have any questions. 

Thanks,

Ramya

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