I'm attending the XGen congress in San Diego this week, and a concept I kept hearing was that for large indels, somatic mutations, CNVs, etc. WGS is the only way to go and that targeted seq or exome capture just won't give you a broad enough view. I expect this message from Complete Genomics, but was surprised to hear it from many others.
In my own experience, while inferring large indels, CNVs is difficult with exome or targeted seq, it isn't an impossible task. While I can see advantages to WGS for CNVs especially, I don't think you can just write off exome/targeted approach carte blanche.
What has been your experience - is exome too narrow for large indels, CNVs, somatic mutations, or do you find if you know what you're doing it can be done?
In my own experience, while inferring large indels, CNVs is difficult with exome or targeted seq, it isn't an impossible task. While I can see advantages to WGS for CNVs especially, I don't think you can just write off exome/targeted approach carte blanche.
What has been your experience - is exome too narrow for large indels, CNVs, somatic mutations, or do you find if you know what you're doing it can be done?
