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Question: Retrieving SNPs coordinates
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gravatar for danatzf
3.4 years ago by
danatzf • 0
Israel
danatzf • 0 wrote:

Hi,

 

I want to know if Galaxy offers a tool where I can upload a list of SNPs and get back their genomic location as coordinates in the correct track

Thanks

Dana
galaxy • 1.4k views
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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by danatzf • 0
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gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Do you have a VCF dataset of the SNPs or a list of rs numbers? And do you wish to compare these to other known annotations or something different?

If you have a list of rs numbers, these can be compared to a dbSNP dataset to obtain the genomic position and other details. Extract the dbSNP table from UCSC (under "Get Data"), then use the tool Join or Compare in the tool group Join, Subtract and Group. From there you can compare the data using genomic coordinates to any other dataset also mapped to the same genome.

For other manipulations involving VCF datasets, including specialized tools that perform comparisons to functional predictions, see the tool groups VCF Manipulation and NGS: Variant Analysis.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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