Get PGX results from VCF including SNV and CNV/SV data

[yaronmaz]

Hi,
I know that NGS flow that starts with BAM can calculate PGX by calling SNV and CNV Coverage and its working great.
What about the flow that the user has SNV VCF and SV/CNV VCF with potential relevant calls. Is there an option to call for PGX with the VCF(s) (can combine them of course as well) that will take into account the CNV/SV calls as well? or is it limited to only the SNV variants?

I saw the chip option, we have scenarios where we have ThermoFisher VCF that has already the CNV reads as well as the SNV ones, and I wonder how I can utilize pyPGX to properly call for PGX results.

thanks
Yaron

[sbslee]

Hi @yaronmaz,

Thank you for your interest in PyPGx. Integrating external SV/CNV calls into the PyPGx pipeline has been asked a few times previously (see #56, #95, and #158). Long story short, it's easier said than done. Theoretically, if you can build a mapping table between external SV/CNV calls and PyPGx calls—such as Normal, WholeDel1, and WholeDel1Hom for the CYP2D6 gene—then it should work out of the box. However, the table-building part is tricky because someone has to actually map every SV/CNV call in your VCF to PyPGx calls first. I'd be more than happy to provide support in this regard, but none of those who approached me with the idea have actually followed through, even though I offered my support ;)