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?
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/
-Bill - GDC User Services Team