We are doing whole genome sequencing using Illumina Hiseq 2000. We are now interested to study the exome part of the whole genomic data but I read in some article http://www.ncbi.nlm.nih.gov/pubmed/21947028 that whole genome misses some variants which exome sequencing is not! Can anybody say whether Illumina Hiseq 2000 is able to cover everything of exome in WGS that is covered by exome sequencing sepwrately?
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Thanks, -
You should re-read that article. Whole-genome sequencing misses variants that exome sequencing finds largely because of read depth. It still costs a lot to sequence a whole genome to the same depth at which one can economically perform exome sequencing. If you have the money and sequencer capacity to sequence the whole genome to the same depth, you'll probably find more or less the same variants. -
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