I'm trying to do variant calling on sequencing data (Illumina Hiseq) resulted from whole-genome sequencing of a given population via GATK. The sequencing technology and bioinformatic packages upgraded regularly; also, some regions in the human genome show high sequence divergence from the reference genome, specifically, it can be true for genome sequencing of a given population as in my case. That's why performing base quality score recalibration (BQSR) before running the HaplotypeCaller on my BAM files is so unclear and confusing to me. In your professional view, running BQSR on my samples can be beneficial or deleterious? Could you please share me your helpful suggestions and help me to make a right decision?
Thank you in advance