I cant find the TCGA variant calling benchmark 4 at https://cghub.ucsc.edu/datasets/benchmark_download. Are the files still on cghub? where can I find the benchmark data?
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hoseintoossi •
You probably have worked this out already, but I'll post this for others:
Instructions on downloading the Benchmark 4 files can be found here: https://gdc.cancer.gov/resources-tcga-users/tcga-mutation-calling-benchmark-4-files
Downloading the files with the manifest requires the GDC Data Transfer Tool. It can be downloaded/ installed here: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool and documentation is available here: https://gdc-docs.nci.nih.gov/Data_Transfer_Tool/Users_Guide/Getting_Started/
Best,
-Bill - GDC User Services Team
They moved everything to the GDC: https://gdc.nci.nih.gov/, not sure if you'll be able to find what you're looking for.
Did you manage to find them? I used these data in a workshop recently and wanted to give the link to where to download the data, only to find they had disappeared!
I have no idea how to find previous TCGA files on the GDC portal.
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If you checked the program name in CGHub manifest, what are those files labelled? I am pretty sure all live TCGA data are in GDC legacy portal now. If they are not program "TCGA", GDC may have either back them up somewhere, or haven't imported them at all. I don't think you can get them easily.