Bases shown despite matching the reference

Question

Closed this issue 3 years ago · 2 comments

Bases shown despite matching the reference. Is this an indicator of low base quality score?

Answer 1 · 2021-04-16T16:56:30.000Z

I just saw another example of this, and it's not related to base qualities.

Answer 2 · 2021-04-16T22:33:09.000Z

From a discussion with Egor - these are soft-clipped bases, and so aren't used for repeat genotyping.