I'm trying to make GATK UnifiedGenotyper to detect indels inserted by wgsim short reads simulator.
Broad employees just informed me that indels are not called because wgsim creates reads of Q17 and everything below 20 is thrown away.
I checked the fastq files, and indeed, all qualities are "2" which is if I understood well the ASCII translation corresponds to 17.
Is there a way to make wgsim output reads with a configurable base quality?
I thought that a trick could be to replace these "2222...2" strings by somthing like "????...?" Or is there a more elegant way to proceed?