chapmanb/cloudbiolinux — comment on commit 77b8cc5bee00e8600b1f08a451789e4cdf9e934c
File:  line 0
By pjotrp:

In that case a dataset should mask - but retain a catch-all sequence for masked repeats. The catch-all should be marked to show low likelihood, and indication of repeat length. Would safe real time on the assembly and other routines. Easy and early data reduction. But OK, I guess it is not a real cost until we look at millions of individuals.