Base recalibration & realignment without known sites
Dear GATK team,
Thanks a lot for the new GATK version and GATK forum!
I am trying to use GATK for yeast strains. I do not have files of known sites of SNPs/indels.
I understand that the BaseRecalibrator must get such a file.
Do you suggest to skip calibration and realignment, or is there another way to go here?