BQSR is recommended at least by GATK's Best Practices and Good laboratory practice for clinical next-generation sequencing informatics pipelines. Heng Li claims that
...BQSR and indel realignment...may make difference on low-coverage data or when the base quality is not well calibrated.
Currently I don't use BQSR, because, frankly, I don't quite understand the point of using it. But maybe I should give it a try? How do I know if the base quality is not well calibrated?