The PI with whom you are working (and under whose ethics-board approved research protocol you've no doubt already consented the study family for these experiments), should know this information. Have you asked him/her
There are many companies around the world that provide whole exome sequencing as both a clinical service and/or as a research service. In the US, clinical whole exome seq for a trio runs about $4K - 6K US, depending on the lab -- that typically includes the library prep, sequencing, as well as (often closed-source) bioinformatics analysis. Research sequencing is also offered by a number of companies in the US, as well as many many academic genome centers (so, it depends on where you are & who you know & who you want to work with). Target capture and sequencing of an exome in an academic center can run around $1200 to $1500 US per sample (paired-end, 100 bp reads, mean read-depth ~100x), sometimes cheaper if you have a research relationship with that lab.
Most of the commercial and academic labs also have the ability to design or help you design targeted exon seq, if you only want to focus on specific regions. In my experience, the commercial targeted capture solutions are more expensive than the whole exome seq (which is also a targeted capture of course), unless you are able to work with one of the newer molecular inversion probe protocols, or are working with a lab that can do this. As for analysis, most academic labs charge something for it in some way (although it can be done as a collaboration, again depends on the PI to PI relationship), or you could do the analysis yourself. The queue in an academic center for any of this work can be really long, especially if you do not have a research relationship with them & it's only one family that you are sequencing. Again, it really all depends on who your PI knows and wants to work with. I really think you should be having this conversation with your PI.
