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This includes the ability for the VCI to automatically update any previous ClinVar submitted Variant Interpretations with the ClinVar SCV id and url as soon as the data is published in ClinVar. This w…
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**Is your feature request related to a problem? Please describe.**
The current intervar is not up to date.
**Describe the solution you'd like**
- [x] #188
- [x] #190
- [ ] implement remaini…
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It's not clear how the tool behaves on gVCF data. The notation is probably simply ignored and harmless but there may be implications for the interpretation strategy. For example, if a second hit is p…
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As discussed in issue #22 (Variant Pathogenicity Interpretation Definition and Scope), we decided that variant origin will be captured as a qualifier, and that this value should be constrained to germ…
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@julesjacobsen given the lack of strictness in the semantics of version 1 variants, it seems it might be better to emit a warning here that the user will need an implementation specific way of doing t…
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Full name of submitter (unless configured in github; will be published with the issue): Hubert Tong
Reference (section label): expr.cast
Link to reflector thread (if any): N/A
Issue descripti…
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As an idea for a dataset with a "story", we could use mapping of diseases in dog breeds, which can be done with a simple filtering for fixed mutations in the disease group (kind of like a very simple …
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I am not able to fully understand the use of the Strand bias filter and RMxN(R3X6) filter in case of somatic variant calling.
For eg.: 1. how the RMXN filter works when a variant is found in the fo…
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#2036 introduces a new syntax to explicitly specify the format of an imported file. Before, this would be just guessed from the extension of the file, which has obvious limits.
This issue aims at b…
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Mechanism for handling obsolete MONDO terms. When there is an obsolete MONDO term then:
- new GDMs should not be able to be created with obsolete MONDO in the GCI
- GDM/variant interpretation snapsh…