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Old 10-26-2011, 11:39 AM   #1
johnsequence
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Location: california

Join Date: Jan 2010
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Default annotation file for maq snp calling

Hi everybody,

An old question but I do not know. How to annotate a SNP profile filtered by MAQ(e.g.final.snp), such as gene symbol, coordinate of exon, and nonsynonymous SNVs. I do not mind writing a simple script to annotate it but where I can download a comprehensive annotation file for hg18. In addition, can I use the count/coverage -depth to infer copy number of the snp? Although I have worked for RNA-seq for a while, but new in DNA stuff. Any advice will be appreciated. Best, John
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