Add an option to restrict BaseRecalibration
The base recalibration step of the pipeline can take up to 7 hours for WGS samples, which is a significant part of the total run time. The developers of GATK state that BQSR requires at least 100M bases per read group: "We usually expect to see more than 100M bases per read group; as a rule of thumb, larger numbers will work better." A human WGS sample with an average read depth of 43x has almost 1300 times that amount of bases. The analysis of these samples would be sped up greatly by restricting BQSR to a single chromosome.