cBioPortal has a number of semi-proprietary files types used to import data into the portal, including discrete copy number data, continuous copy number data, and segment data.

cnvkit.py outputs a number of file types that should, ultimately, contain everything needed to create the above cBioPortal input files - however, a lot of conversion processing is needed. The cnvkit.py files I have include...

• control001-01.antitargetcoverage.cnn
  • control001_reference.cnn
  • control001.targetcoverage.cnn
  • metastasis011.antitargetcoverage.cnn
  • metastasis011_BAF.tsv.gz
  • metastasis011_BAF.tsv.gz.tbi
  • metastasis011_BAF_withAltBases.tsv.gz
  • metastasis011_BAF_withAltBases.tsv.gz.tbi
  • metastasis011.cnr
  • metastasis011.cns
  • metastasis011_gainloss-genes.txt
  • metastasis011_gene-breaks.txt
  • metastasis011_igv_track.cn
  • metastasis011_ploidy_purity_2D.txt
  • metastasis011.targetcoverage.cnn

Can anyone offer a tool/guide/assistance for converting these files from cnvkit to cBioPortal?