Our lab is going to do Sanger sequencing of clonal viral isolates from some infected patients. The question that has been asked is what is the accepted method for establishing confidence levels around the detection of a 1 percent minor variant by picking X clones for sequencing?
In other words, how many clones do we need to pick per patient so that we can be very confident that we can still detect a minor virus variant, even if it is present at only 1% frequency among the patient's viral load?
I am hoping that this is a pretty common problem and that is has been solved (and published) somewhere, although I can't seem to find any useful references.
References, equations, ideas, comments are welcome.