Targeted sequencing

[ulz_peter]

Hi,

we are planning to do targeted resequencing for genetic diagnostics in our laboratory using the FLX instrument with titanium chemistry.
I now wonder if I should align the results (we do not have results yet, only theory) against the whole human genome or if it's enough to align against the targeted genes?
Peter

[NextGenSeq]

We usually align against the genome since with Agilent whole exome sequence selection you get ~100 bp of flanking intron sequence. You can detect mutations affecting splicing by including the intron sequence in your alignment.