How can I find SNPs between two Genomes?

Question

[Zeason]

Here I have two fasta files of two genomes.

I want to find SNPs between them , how can I do it ?

Can GATK do it ?

[Santosh Anand]

Are they the same species, just differing by SNPs?

[Zeason]

yes,they are same plant species. but they are different lines.

Answer 1

[Tm]

Have a look at similar previous post. And if your aim is to look into difference between both the genome then you can use Nucmer from Mummer followed by Assemblytics.

[Zeason]

thanks a lot.I will try it.