Hi everyone,

For an allele mining project I need to generate in silico NGS data. I have chosen to use Grinder
to do so. I would like to add randomly generated SNPs to my reference genome, is any software
available to do that ?

Thanks for help!
You could try `mutate.sh` from `BBTools/BBMap`. `mutate.sh` can also produce a VCF file of the SNPs added. You can also generate random Illumina reads with the BBTool `randomreads.sh`
https://sourceforge.net/projects/bbmap/