Hello, the data_fusions.txt file in the cbioportal_files for the NSCLC data is in a depreciated for format for loading into cBioPortal. They now require the fusions be in Structural Variant format as described in their documentation -- [cBioPortal Structural Variant Format](https://docs.cbioportal.org/file-formats/#structural-variant-data). I reviewed the data in the data_fusions.txt file to attempt to convert it to SV format but I am not sure this would possible with only the data in the file. Would it be possible to generate the SV file from the source data?
Created by Justin Levens jstnlwork @jstnlwork
Hmm that is interesting. Noted. I am glad you were able to work something out!
Let us know if you have any other questions!
Best,
Chelsea Hello Chelsea,
Thanks for sharing! I didn't know this tool existed but it appears to work. Strangely, the tool within the GENIE-fusion-to-sv-converter doesn't appear to output the file in the correct format, but the tool in the root does. Thanks again!
Justin Dear @jstnlwork,
Thank you for your interest in the GENIE data!
Have you tried using this tool? https://github.com/cBioPortal/datahub-study-curation-tools/tree/master/fusion-to-sv-converter
Best,
Chelsea