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On allele page for something on MT, eg CA337095804:
* Click on the g.HGVS in the GRCh37 or GRCh38 column
* Expected is to go to the variant page showing that build
* Instead, it loads your default bu…
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Consider an upstream HGVS such as "NM_000133.4(F9):c.-53A>G" (-26)
The HGVS guidelines say it's upstream and shouldn't use the transcript to classify. However, people do report it that way.
* VEP wi…
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The HGVS nomenclature now recommends including both a sequence and transcript identifier for some variants, with the transcript identifier in parentheses e.g.: https://hgvs-nomenclature.org/stable/rec…
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mavedb-api has a couple of optional dependency categories, `dev` and `server`.
The `server` dependencies are required to run the database, but not required to use the models for projects like [Mav…
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**Is your feature request related to a problem? Please describe.**
Currently the entry for Variant Validator in Variant Info page is empty. We need to fix it in order to provide a possibility to acce…
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As you know some variants have multiple NM_ coded transcripts. For example in this variant http://myvariant.info/v1/variant/chrX:g.153296529G>T, there are 7 different HGVS coding transcripts.
Is My…
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## Describe the issue
VEP performed incorrect pHGVS annotation for the variant `NM_173660.5:c.1124_1127dup (rs606231128)` .
VEP annotated the variant as `NP_775931.3:p.Ala377ProfsTer31` when the cor…
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**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**…
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* Generate 100/1k/10k random HGVS from ClinVar
* Install SeqRepo locally
* Benchmark how long it takes with JSON and REST client - check out caching/non caching etc
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**Describe the bug**
I get an error message of `AttributeError: 'AARefAlt' object has no attribute 'ref_n'` when using `validate()` against a protein variant.
**To Reproduce**
Steps to reproduc…