I have illumina sequencing for 6 isolates and after mapping them to a reference, I obtain a VCF file for each isolate.
I have previously asked how can I use these VCF files to obtain a phylogenetic tree and was suggested to try the R package SNPRelate. I am a bit new to this, and understand that in using SNPRelate I need to convert my vcf to gds format, after which I need to perform LD pruning. I have tried to look this up in many sources, but still do not understand how SNP clusters can affect my phylogenetic results?
Thank you, Adrian