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ysbioinfo / NeoSV

A computational workflow to identify neoantigens from structural variations (SVs)
MIT License
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SVs file in VCF format #2

Closed immuneAI closed 6 days ago

immuneAI commented 6 months ago

Hello, Thank you for this great tool, is there any approach to convert SV's file with breakpoint positions into NeoSV required VCF format?

ysbioinfo commented 6 months ago

Hi @immuneAI , Thanks for your interest. Only the position of breakpoint is not enough. NeoSV also need the orientation of that breakpoint, thus to make sure how to join two transcripts. What is the format of your SV file?

Yang

immuneAI commented 6 months ago

Yes, I do have orientation in my file attached here in tab sep columns SV_file.txt

ysbioinfo commented 6 months ago

Hi, The file seems containing all necessary information, but unfortunately I do not know a tool to transform it into VCF format. I am planning to upgrade NeoSV to make it compatible with BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format). Your file is similar to the BEDPE format and should be easy to transform. Not sure if you can wait to that time, since it will take me 4-6 weeks to complete it.

immuneAI commented 6 months ago

Hello, That would be a great help!! Looking forward with BEDPE format & happy to try it.

ysbioinfo commented 5 months ago

Hi @immuneAI , The newest NeoSV v0.0.4 has been released. It now supports BEDPE format. I also attached a template file here (https://github.com/ysbioinfo/NeoSV/blob/main/test.sv.bedpe). You can have a try by installing the newest version from PyPi or GitHub.