dbSNP updates and the effect on variant annotation results

warrenemmett · 10-18-2011, 12:31 PM

Hi there,

I have had several queries from users checking my snp annotations (i use both ANNOVAR and SNPeff) and tell me that a large percentage of their candidate SNPs that are called as unknown snps are actually present in the dbsnp 135 database.

I have checked both annotators and neither have updated past 132. I know its possible to include these databases manually but before I take the plunge I just wanted to hear opinions if this is actually so critical (and if there isnt good reason it is currently excluded), surely the newer versions of dbsnp still contain errors and are relatively unstable? Any opinions on this would be appreciated.

Thanks!

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10-18-2011, 12:31 PM	#1
warrenemmett Member Location: South Africa Join Date: Nov 2008 Posts: 23	dbSNP updates and the effect on variant annotation results Hi there, I have had several queries from users checking my snp annotations (i use both ANNOVAR and SNPeff) and tell me that a large percentage of their candidate SNPs that are called as unknown snps are actually present in the dbsnp 135 database. I have checked both annotators and neither have updated past 132. I know its possible to include these databases manually but before I take the plunge I just wanted to hear opinions if this is actually so critical (and if there isnt good reason it is currently excluded), surely the newer versions of dbsnp still contain errors and are relatively unstable? Any opinions on this would be appreciated. Thanks!