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Old 01-10-2016, 12:39 PM   #1
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Default Is there a way to compare the genomic locations of mutations for legacy transcripts w

Hi all
I have a list of variants described in hgvs format. The variants relate to old versions of transcripts. I want to translate these variants into genomic locations. I have previously used Mutalyzer to perform this task. However I am unable to perform this task using Mutalyzer with older versions of transcripts. So for example with the transcript


There is no record returned in the current version of mutalyzer but there is for transcripts NM_003002.2, NM_003002.3.
Does anyone know how i might be able to return the genomic location for this old transcript version please.
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Old 01-10-2016, 12:57 PM   #2
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Old 01-11-2016, 09:42 AM   #3
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TransVar is a reverse annotator for inferring genomic characterization(s) of mutations (e.g., chr3:178936091 G/A) from protein or cDNA annotation(s) (e.g., PIK3CA p.E545K or PIK3CA c.1633G>A). It is designed for resolving ambiguous mutation origins, arising from alternative splicing.

TransVar has the following features:

supports HGVS nomenclature
supports both left-alignment and right-alignment convention in reporting indels.
supports annotation of a region based on a transcript dependent characterization
supports single nucleotide variation (SNV), insertions and deletions (indels) and block substitutions
supports mutations at both coding region and intronic/UTR regions
supports transcript annotation from commonly-used databases such as Ensembl, NCBI RefSeq and GENCODE etc
supports UniProt protein id as transcript id
supports GRCh36, 37, 38
functionality of forward annotation.

Citation: Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multi-level variant annotator for precision genomics. Nature Methods. In Press.
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hgvs, mutalyzer

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