Benchmarking Read Alignment And Variant-Calling Algorithms (For Dummies)

Hi all,

I am wondering if there is a good step by step guide of how to benchmark alignment and variant calling software. I do understand the premise e.g.

Generate reads with known mutations
Align to genome
Assess accuracy
Perform variant calling
Assess accuracy

However I have some kind of intellectual disconnect when I try to think about how to actually do it. Too much time in industry and not enough in academia I suspect!

Can anyone point me in the right direction?

Thanks in advance!