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### Description of feature
This time I tried to look through issues and code. ;)
As far as I can see, sarek does not do any kind of variant decomposition, which (if coupled with normalization) can…
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### Tested versions
- Reproducible in: v4.3.stable.official [77dcf97d8]
### System information
Godot v4.3.stable - Windows 10.0.19045 - GLES3 (Compatibility) - NVIDIA GeForce GTX 1060 6GB (NV…
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Hi,
With gatk 4.6.0 and Funcotator data sources v1.8, and output in VCF format, I'm seeing some annotations with strange character combinations inside of them:
"_%7C_"
"_%20_"
For example for on…
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I have already been using Adam with snpEff annotations and it worked great. However, when I've tried to use it with a VCF file annotated using Ensembl VEP it didn't work. I was expecting, that ANN for…
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Caching VEP annotations (instead of re-running VEP on all variants each time) would speed up the ClinVar pipeline. This would be nice for updating ClinVar data more frequently.
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VCF has been extended to include a bunch of other annotations for the effects of a given variation. The resulting GA4GH messages are `VariantAnnotation` `VariantAnnotationSet` `TranscriptEffect` `Anal…
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When dealing with some serialization libraries, it's required to add annotations to structs, enums and variants. There are currently three PR fixing this issue, could the maintainers review them and m…
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Example, 1:g.69918522A>T is an intergenic variant and the annotation pipeline returns empty. When importing to the portal, the variants are filtered out by the Variant_Classification column. Any varia…
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The value "Red_Zone" in th confidence column of the Kestrel_concat dataframe is never assigned or defined and only used once.
What does this do?
```python
Kestrel_concat = Kestrel_concat[Kestrel…
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## Describe the issue
We noticed a variant, a single base insertion after the first position of a gene, getting annotated as an upstream_gene_variant with respect to that gene. The distance is then…