Hello Atteeq,

The general path would be to:

1) get dbSNP data & format 2) upload your own data & format 3) compare

Use "Get Data: Bx Main" to obtain dbSNP data. Format using tools in "Text Manipulation" to reduce content to a simple BED (Interval) file. Format your own data to be in a similar form. Then use tools from "Operate on Genomic Intervals: Intersect/Subtract/etc.". Or format so that the dbSNP data form mirrors your own and use "Join, Subtract and Group: Subtract Whole Query" for the comparison.

A simplified comparison history with multiple example outputs is here: dbSNP 130 vs dbSNP 131: hg19 chrom 10: http://test.g2.bx.psu.edu/u/jenjackson/h/snp-subtract-example-8-2-2010

More SNP specific tools to explore: NGS: Indel Analysis SNP/WGA:*

Thanks,

Jen Galaxy Team

On 7/31/10 11:26 AM, Rehman, Atteeq (NIH/NIDCD) [F] wrote:

Hello,

I have a list of variants(SNPs) that differ from reference sequence (in my human subject DNA) and I want to filter out the known variants reported in dbSNP, so that I can have a short list of putative novel variants. Could somebody please tell me how can I do this?

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*Atteeq Ur Rehman*

Visiting Fellow

National Institute on Deafness and Other Communication Disorders,

National Institutes of Health,

Room 2A-19, 5 Research court, Rockville, MD, USA, 20850.

Lab Ph. No. 301-402-9059

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