Can SCmut be adapted to calling SNVs from scWGS?

[nyuhuyang]

Can SCmut be adapted to calling SNVs from scWGS (single-cell whole-genome sequencing)? Are their any parameter should be changed or we can use it directly?

[nghiavtr]

Dear nyuhuyang,

Thank you for interesting in SCmut.

Yes, SCmut is generally applicable to scWGC data since the statistical model is not too much dependent on the specific features of scRNA-seq.

However, since we have not yet tested the method to scWGC so I can not give specific suggestion for the parameter adjustment. So when applying it, please read carefully the parameters in scfdr() function. I think some parameters might need to consider are:

• vaf.cut ( threshold of the vaf: If vaf<cut then fdr=1): it would be different in scWGC because you get lower copies of input (two copies of DNA)
• nrep and nr might also change the performances

I hope my suggestions would help, and good luck with your research.

Best, Nghia