How to create alternate reference for SNPs?

Question

[Parham]

Hi,

I am looking for ways to create alternate references for metagenomes. I would like to introduce SNPs every other x base pairs in the new reference using the original reference. Ideally if there is a package that does this, I appreciate to know about it, otherwise what is your recommendation to do it?

[GenoMax]

If you have the reference then mutate.sh from BBMap suite can introduce mutations that you control. It will also make a corresponding VCF. If you would like to simulate the meragenome itself first then randomreads.sh from BBMap can do that with metagenome=t flag.

[Parham]

Thanks! Yes, I have the reference and the idea is to make an alternate version of that reference with introducing mutations. If you have experience with mutate.sh I wonder if Substitution rate, 0 to 1 means 0.1 will replace 10 percent of bases?