short kmer or long kmer with SNP inside ?

Question

[sebastien.letort]

I'd like to seek for SNP that are close to each other.

I think I can use a small kmer size like 11 or use longer kmer (k=51) but add the -P=4 option. I'm not sure to well understand the differences. Can you help me?

I'm working on complex genome (plant with lot of duplications)