This builds on prior question http://www.biostars.org/post/show/11990/genotype-data-and-exome-sequencing-data-sensitivity/
If I care only about variants covered by dbSNP with an rsXYZ number and assuming I could do two things on a single clinical patient:
A) genotyping with some array (e.g., Affymetrix with 1M SNPs)
vs.
B) exome sequencing, and filtering the resulting VCF file to only variants covered by dbSNP and of high quality
Which one will be more accurate?
I know that B can give me more data about indels and such but my clinical-implications-of-genome-data-knowledge-base gives me clinical advice only if it is a previously known variant. So I am more after a method which is most accurate. In fact I only need to know if the sequencing will be at least as accurate as genotyping. (assuming "average" sequencing vendor and pipeline)
What is the biologic question you are trying to answer? Exome sequencing will actually give much less data about variants that a 1M snp array, but the 1M snp array may not give you the information you want.
as far as I know after finding a significant variants by exome sequencing you should confirm it by sanger sequencing method.On the basis of read number you can decide about the sequence related to specific region if read number is good you should confirm by sanger sequencing.If read number is not enough it might be false result or coverage in that region is not good.