Question: How to create alternate reference for SNPs?
0
gravatar for Parham
28 days ago by
Parham1.5k
Sweden
Parham1.5k wrote:

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?

reference snps • 80 views
ADD COMMENTlink modified 28 days ago • written 28 days ago by Parham1.5k
1

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.

ADD REPLYlink written 28 days ago by genomax92k

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?

ADD REPLYlink written 28 days ago by Parham1.5k
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