Qualities of bases accepted for local realignment
Dear GATK team,
I try to adjust Solid data to run in GATK. Unfortunately the problem is qualities of bases. I tried to adjust all of them to Illumina format (+33) but it seems they are not accepted during the following step:
2. Perform realignment of the target intervals
How can I adjust my qualities (or optionally whole Solid data) to work fine with GATK?