We have ongoing outsourced deep exom-sequencing of ten samples and our question is when we receive the data should we align to the reference hg18 or hg19? What are the pros. and cons. for using the more stable hg18 compared to the updated hg19?
I know from previous questions that hg18 has more annotation, however does that matter in the alignment process?
Any comments are very welcome... Thanks a lot.