BQSR - perform on whole genome or single chromosomes OK?
I am running GATK Best Practices again and just wanted to assure myself that I am proceeding correctly. I remember reading somewhere on here that BQSR performs best when given the whole genome to work with (similar to VQSR in that respect). Better to just run using the whole genome rather than giving it single chromosomes. I couldn't really find this comment/recommendation when I tried to look for it again, so wanted to see what the final word was on this. How should one proceed?