How to use BBmap (mutate.sh) to simulate the human genome?

Question

[kamanovae]

Hi! I want to simulate the human genome. I found a suitable BBMap mutate.sh) program. The mutate.sh only outputs reads that contain mutations. But I need to get a fast output file that would contain reads with mutation and without mutations. I want to try to maintain the coverage of the reference genome. How can i do this?

Now I use the command to run:

1.bbmap/mutate.sh in=reference/gh19.fasta out = reference/hg19_with_mut.fasta id = 0.99 prefix = bbmap

I can use the program BBMap randomreads.sh) , but it looks much more difficult to run and I'm afraid to unconsciously get an undesirable result

[GenoMax]

One does not really simulate a genome but you simulate reads using the reference for that genome. randomreads.sh is not difficult to run.

Do you need to simulate a genome at this point? There are plenty available in databases. You can run mutate.sh on one of them to introduce the mutations, if you don't want to simulate a new dataset.

[kamanovae]

At this stage, I need to introduce mutations in the reference genome, and then I plan to use the NanoSim program to simulate nanopore reads. My final goal is nanopore reads with introduced mutations. Which program is better for the first step?

[GenoMax]

Then use mutate.sh.

Written by Brian Bushnell
Last modified August 6, 2019

Description:  Creates a mutant version of a genome.

Usage:  mutate.sh in=<input file> out=<output file> id=<identity>

I/O parameters:
in=<file>       Input genome.
out=<file>      Output mutant genome.
vcf=<file>      Output VCF file showing variations added.

Take a look at processing parameters to control the mutations.