Using ONT tumor/normal samples output from wf-human-variant --phase and Sevrus

[amarkez]

Hi,

I’m working with ONT data for variant analysis using the wf-human-variant pipeline.
I’m running both tumor and normal samples separately through the workflow with the --phase option enabled.

I’m not sure whether the outputs produced in this way can be directly used in Sevrus, or if some of the earlier steps need to be repeated/adjusted for tumor–normal analysis.

Thanks!

Ana

[aysegokce]

Hello Ana,
You can use the phased VCF from the normal sample to re-haplotag the tumor with WhatsHap. After that, run Severus with the re-tagged tumor and normal BAMs from the pipeline, along with the phased VCF from the normal run.

Let me know if you have any additional questions!
Best
Ayse

[amarkez]

Thank you for the quick response, I appreciate it! I will try it and will get back to you if I have any further questions.

Best regards,
Ana