On GATK website http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-gatk-accept and their public FTP server, I found a few difference human genome references in their resource bundle: b37, b36, hg18, and hg19. This made me wonder which one I should use for exome-sequencing data analysis?
In my pipeline, I started using BWA-MEM with the hg19 reference, should I stay consistent for the same reference with GATK? or it seems to me Broad Institute people recommend using b37, as they said hg18, b36, etc were lifted over from b37 - confused here. thanks