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Does GenomeBrowse display the coding designation for a particular base?

asked 2015-10-07 22:12:01 -0700

I am interested to see whether the either the reference genome or a BAM file I load can display the particular coding designation for a particular base (the CDS). I see that I can identify the amino acid (p.) and can get the genomic location of each base. Thanks.

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answered 2015-10-09 14:37:17 -0700

Hi Paul,

I am happy to help with your GenomeBrowse questions.

Just to clarify are you looking for the HGVS C dot notation (ex. NM_001277333.1:c.562G>T) for all variants in your data? If so there are a few tracks that have this information for their listed variants, for example the "COSMIC Mutations Left Aligned 71 v2, GHI" track provides this information in the Mutation CDS field. This is a cancer specific track so only those cancer specific mutations are included.

If you are looking to have this information for all of your variants then some type of variant classification algorithm is required to determine the position of the variant within gene regions to create the C dot notation. GenomeBrowse does not have this functionality but our analysis software VarSeq can perform this as long as your variants have been called and VCF files produced.

Let me know if you have any further questions or if you would like to give VarSeq a try.

Thanks, Jami...

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Asked: 2015-10-07 22:12:01 -0700

Seen: 238 times

Last updated: Oct 09 '15