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Correct HGVS nucleotide names to be indexed from the start of the reference genome #165

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miseminger opened this issue Apr 26, 2024 · 0 comments · Fixed by #163 or #184
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Correct HGVS nucleotide names to be indexed from the start of the reference genome #165

miseminger opened this issue Apr 26, 2024 · 0 comments · Fixed by #163 or #184
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miseminger commented Apr 26, 2024 •
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Currently, the HGVS nucleotide names from the VCFs, created by SnpEff, give the nucleotide mutation position as referenced from the start of the protein. HGVS recommendations require the position to be given with respect to the reference nucleotide sequence.

So, we can either:

  1. rewrite those positions to match the number in the pos column, or
  2. put the transcript identifier in brackets, eg. NG_012232.1(NM_004006.2):c.93G>T
@miseminger miseminger added the bug Something isn't working label Apr 26, 2024
@miseminger miseminger self-assigned this Apr 26, 2024
@miseminger miseminger linked a pull request Apr 29, 2024 that will close this issue
Make addfunctions2gvf.py compatible with new 'n/a' in "comb_mutation" and 'multiaa_comb_mutation' columns #163
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@anwarMZ anwarMZ linked a pull request Oct 25, 2024 that will close this issue
Adapt to new DH template #184
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@anwarMZ anwarMZ closed this as completed Oct 25, 2024
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