I am currently working on the analysis of whole exome data. I need to align my reads with reference genome. I am wondering if there is any reference exome out there ? As I am using a SureSelect Human All Exon 50Mb Kits, I know what I am currently capturing and sequencing. If there is a reference exome, I could save significant computing time on alignment and further downstream analysis. If no such reference exome available, why it is not a good idea ? or What could be the pros and cons on generating one using GENCODE / CCDS / RefSeq ? Have you tried this before ?
Looking forward for your thoughts.