Convert COSMIC ID to dbSNP id?
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3.7 years ago
biocyberman ▴ 830

I downloaded data from COSMIC database, and now want to do batch conversion of the COSMIC ID to dbSNP id. For example, Cosmid variant: COSM425261 . What is the RS number of this SNP? I tried with biomart but did not work: http://www.ensembl.org/biomart/martview/def67ebf751f91c637ecbb873b20d4d1

SNP COSMIC • 2.7k views
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does your data include chromosome coordinates? If so, you can always try to annotate the coordinates with ANNOVAR and specify both Cosmic and dbSNP output fields. Note that there could be several matching ID's

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3.7 years ago
Denise CS ★ 5.2k

The chances are your COSMIC IDs will not be convertable to rsIDs as the first are somatic mutations, not "neutral" genetic variants from dbSNP. There may be exceptions to this though. Unless the SNP had an rsID to begin with, followed by the observation that is implicated in cancer, it won't be curated by COSMIC and therefore not COSMIC ID would be given. If you use the Ensembl Variant Effect Predictor, you should be able to input your COSMIC IDs and if these co-locate with rs numbers, you will get that in the output file.

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