Heterozygosity with short read simulators?

[andy11]

I was wondering if short read simulators like wgsim (from samtools) create heterozygosity from the input fasta file and if so, what they do to create it.

Thanks for any help

[nilshomer]

Yes, they store two copies of the reference, and when they mutate it (for SNPs/indels), some fraction mutates only one copy. See the source code for details.