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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