A bit technical question here... I want to simulate an heterozygous indel starting from a piece of reference genome (FASTA file) and I thought about the following workflow to do it. Could you comment it? Is it a good idea or is there a better approach?
copy of reference file (let's call it ref.fasta) to ref_insert.fasta
edit ref_insert.fasta and insert a sequence of 10bp for instance,
concatenate both fasta files ref.fasta into a new fasta file (ref_diploid.fasta)
simulate short reads with a simulator (my favorite one is wgsim) disabling mutations generator,
align and then detect variants.