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 ?
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.shhttps://sourceforge.net/projects/bbmap/