Simulating a genome with known SNPs

[lovettse]

Does anyone know of a way to generate a simulated bacterial genome with known SNPs and indels relative to a given reference? I'd like to be able to generate these simulated genomes to benchmark various SNP-calling pipelines. It would, after all, be much easier to trust a particular SNP if I know for an absolute fact that it's there. I'm using PacBio data, so the various tools to simulate short read dataset seem designed to solve a different problem than the one I have.

If you think I'm going about this in entirely the wrong way, I'm willing to listen.

[vivek_]

If you have a VCF file of known variants and a reference fasta, you can use GATK's FastaAlternateReferenceMaker