bioinformatics-ibch / comparison-study-of-germline-cnv-calling-tools Goto Github PK

Hello! Why didn't you just publish your validation set? If you have already done this work? Others could compare other tools too using this set

Hi there,

Thank you very much for the work you did, it's very helpful especially because it's almost impossible to find a ground truth to benchmark CNVs analysis!

I've taken a look to the repo and I didn't understand the input csv files of analysis.py.
These input files are named cnv_calling_tools.sort and the content is a tab separated dataframe of ['chr','start','end','type','length','targets'], but how exactly did you come here?

I used some of the tools (cnvkit, cnmops etc) and the output i get from these tools is a tab separated file different from the input of analysis.py script.

Is there some steps in the middle that I'm missing?

Thank you very much for your help! 🌻

Hi,

thanks for the very interesting work and for providing the code as well!

If I understood correctly, the file validation_set/internal_standard.bed tells me whether or not an exon is considered a CNV exon or a non-CNV exon. Is there any way to also get information if a CNV exon is a deletion or a duplication exon?

Kind regards,
Marius