Call GATK baserecalibrate on readgroup bam files
Base recalibration takes a long time to run. By running the base recalibration on the separate per-readgroup bam files, instead of on the output of the markduplicates step, we can run these tasks earlier in the pipeline, and in parallel with the markduplicates step. This reduces the total runtime of the pipeline. This commit also adds a test to make sure that statistics for both read groups are present in the base recalibration output file.