I have exomes from 24 individual mice. The exomes are the product of Roche's SeqCap EZ HyperCap target enrichment kit. I see that the mouse exome design comes from mm9/NCBI37, the previous major reference genome released in July 2007.
Which reference should I use to align these reads? What artifacts may arise from mapping these reads designed from mm9 to the mm10 reference? I have already aligned the reads to mm10 and noticed an erroneous exon right in the middle of an intron, perhaps a target that was an exon in the mm9 release but revised out of the mm10 release. My goal is to investigate structural variation.