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How to use

>python tcga_cnv_2_ga4gh.py [path of data directiory] [path of meta-file]

>python openCNV_2_ga4gh.py

Arguments

  1. a directiory which has the TCGA data in the orginal folder & file structure.
  2. a JSON file downloaded through the TCGA API, which contains the meta-info of each file

Shortcut

python tcga_cnv_2_ga4gh.py /Volumes/originalData/TCGA/MaskedCNV_2017_10_03 /Volumes/originalData/TCGA/Meta/tcga_masked_cnv_meta_171205.json