Are soft clipped bases used in indel realignmment?

colinhercus

Hi, Some aligners produce Smith-Waterman alignments and may soft clip bases from a read when there are indels or mismatches near the ends of the reads. I was wondering if you include these bases in the realignment process? And if not whether you might consider making it an option? Thanks, Colin

Geraldine_VdAuwera

Hi Colin, No, we don't use those bases, and we aren't planning to make that an option, sorry.