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Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
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Add sample ID to vcf2cytosure #1003

Open christacosta opened 1 year ago

christacosta commented 1 year ago

Hi, Balsamic now creates '.CGH' files which is great. When I download the file it has both Starlims ID and Scout case number in the file name. However, when I open the file in cytosure it only says "TUMOR" [FE file: "tumor.txt"] in the program. It would be great and safer to avoid patient confusion if the file name would show up even in the opened cgh file in cytosure.

dnil commented 1 year ago

Indeed! Thanks a bunch for writing about it! I'll transfer this issue to Balsamic!

khurrammaqbool commented 1 year ago

Thanks, @dnil. Would it be possible to add --sample_id to vcf2cytosure to make it simpler to implement?

dnil commented 1 year ago

Hehe, sure, but there are already two ways to specify them: either as sample IDs in the input VCF, or by giving the ID in the vcf file name. Up to you - if you feel it is easier with an option I can add it!