Paraphase output annotation

[themkdemiiir]

Hello,

Do you have any suggestions to annotate output JSON and VCF files? How can I extract the specific CNV positions? Also, is there a way to convert the VCFs to standard VCF format?

Thanks!

[xiao-chen-xc]

Hi @themkdemiiir, for medically relevant genes, we have some tutorials (listed in the README) on understanding the JSON files. For general annotation process downstream of Paraphase, we recommend annotating the VCF files for variant consequences and then determining the copy number of functional genes in each gene family. We are working on a tool to facilitate Paraphase annotation. If you have questions or suggestions, feel free to share them here or email me at [email protected]. I’d be happy to chat through email or on a call.

[themkdemiiir]

I emailed 🙏
Thanks