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SV Annotation HGVS - wrong version, also was slow, lots of ClinGen errors #1227

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davmlaw opened this issue Jan 14, 2025 · 1 comment
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@davmlaw
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davmlaw commented Jan 14, 2025

I started working on this and committed work under #1222

However I found a number of issues:

  • We were going through the slow process of transcript version bumping / best match etc - which is slow and we do NOT want to do that for annotations HGVS as it's supposed to match the transcript version!
  • The version being used for transcript version was incorrect due to pulling out wrong data from VEP (which is why we were calling ClinGen so much as we don't have those transcript versions)

I fixed all this but TODO:

  • Need to do something that will trigger a fix of existing c.HGVS. Could either re-calculate it (bit more work but probably faster) and bulk update or re-ingest all the annotation (which may be deleted?)
@davmlaw davmlaw added the bug Something isn't working label Jan 14, 2025
@davmlaw davmlaw changed the title SV Annotation HGVS - slow, lots of ClinGen errors SV Annotation HGVS - wrong version, also was slow, lots of ClinGen errors Jan 14, 2025
davmlaw added a commit that referenced this issue Jan 14, 2025
davmlaw added a commit that referenced this issue Jan 15, 2025
davmlaw added a commit that referenced this issue Jan 15, 2025
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davmlaw commented Jan 23, 2025

This was made into management command / migration script: fix_annotation_sv_c_hgvs

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