Hi, I have two hsapiens genome... The first is hg38 and the second is CV. I need to extract the SNPs and INDELs comparing CV with reference to hg38. 

How I could do this?

Thanks for your help!!!

Hi,

If you have the chainfile that describes the pairwise alignment between hg38 and CV, I think it would not be too hard to use it to extract the SNPs and INDELs. If you don't, then you need to align the 2 genomes first. I'm not aware of tools in Bioconductor that can perform this kind of alignment though. Neither pairwiseAlignment() in the Biostrings package nor msa() in the msa package will scale to the size of a Human chromosome. You'll need to look outside Bioconductor for a tool that handles this. I found this

https://www.biostars.org/p/114535/

on Biostar but it's not clear that this solution works on a big genome like Human. Maybe you'll have better luck.

Cheers,

H.