Does GATK proposes something to deal with homopolymer indels?
I used qualimap to evaluate the qualimap to the BAM files (10) which I got by using the GATK best practices pipeline.
It seems that the mean of homopolymer indels percentage for my ten files is 70%. Is it normal? I am quite new for this.
We thought that BQSR can correct it. Is it possible? have you already encountered this kind of problem?