Hi Biostars,

I am looking for a tool to introduce variants in a reference genome. 

**The ideal tool I am looking for:**


*Takes as input:*

 - genome fasta

 - a vcf file

*What it does:*

 - Insert some of the variants (randomly) present in the vcf into the reference genome

*What is the output*

 - The ideal output would be a mutated new reference fasta, and a vcf file (The vcf file is not that important).

The reason I am looking for this is because I am working on simulation tool, but I would be happy to rely on a third party software to introduce the mutations.


cheers,
Not exactly what you are asking but if you are not wedded to specific vcf files then you could go the other way by using `mutate.sh` from BBMap suite. Lots of processing parameters you can control.

    $ mutate.sh
    
    Written by Brian Bushnell
    Last modified December 13, 2018
    
    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>      VCF file showing variants added.

