Answers.Body: <p>Neither <code>C1092T</code> nor <code>OPG001:D162N</code> seem to follow HGVS conventions. You could try to convert them to HGVS nomenclature standards then use modules such as <a href="https://hgvs.readthedocs.io/en/stable/" rel="nofollow noreferrer">hgvs</a> to get amino acid changes from nucleotide changes. You will need reference sequence identifiers though, so it might be easier to go from chromosomal level changes to AA changes, as cDNA changes depend on the transcript (which may or may not be an issue with viral transcripts).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-27T15:31:02.773Z
Answers.LastActivityDate: 2023-03-27T15:31:02.773Z
Answers.UserDisplayName: Ram RS
Body: <p>I have the sequencing data of a Monkeypox virus sample. I have the list of variants extracted from Nextclade and I want to find the corresponding aminoacids substitution.
  For example I have the variant C1092T (nucleotide annotation) and I want to automatically convert it into OPG001:D162N (aminoacid annotation).</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-27T11:21:09.517Z
Comments.Text: Please could you provide a reproducible example of the problem you face?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-28T06:27:34.773Z
Comments.Text: https://www.ensembl.org/info/docs/tools/vep/index.html
Comments.UserDisplayName: Matteo Ferla
Tags: <ngs><snp><format-conversion>
Title: Variants list to aminoacids
ThreadText: # Variants list to aminoacids
  
  (Asked by: username_0 on 2023-03-27)
  
  I have the sequencing data of a Monkeypox virus sample. I have the list of variants extracted from Nextclade and I want to find the corresponding aminoacids substitution.
  For example I have the variant C1092T (nucleotide annotation) and I want to automatically convert it into OPG001:D162N (aminoacid annotation).
  
  **Tags:** ngs, snp, format-conversion
  
  > **Comments:**
  > **username_1**: Please could you provide a reproducible example of the problem you face?  
  > **username_2**: https://www.ensembl.org/info/docs/tools/vep/index.html  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-03-27. Score: 1
  
  Neither `C1092T` nor `OPG001:D162N` seem to follow HGVS conventions. You could try to convert them to HGVS nomenclature standards then use modules such as [hgvs](https://hgvs.readthedocs.io/en/stable/) to get amino acid changes from nucleotide changes. You will need reference sequence identifiers though, so it might be easier to go from chromosomal level changes to AA changes, as cDNA changes depend on the transcript (which may or may not be an issue with viral transcripts).
  
  
  ---
  
  