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!