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I faced a use case where inheritance for `@EnabledIfSystemProperty` would have helped for less boilerplate.
Specifically, it's a project with many test classes for integration tests that should be ex…
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I'm trying to integrate a custom BED file as a custom database in Ensembl VEP, but I am not getting the expected results. The BED file I’m using has a value for each base position, not a variant-speci…
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Background: first I found Sama-COCO in FiftyOne dataset documentation, then I searched Sama-COCO in Google Scholar. There, I [found your paper about COCONut dataset](https://arxiv.org/abs/2404.08639).…
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In quantitative genetics it is common not to treat alleles at a locus as equal. The "functional consequence" of each allele is important and the process for determining these consequences is well sta…
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Variant annotation sets provide transcript effect data for variants. By creating summary statistics for a variant annotation set we gain some understanding of the distribution of coding vs. non-coding…
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Dear Developers,
I have my vcf file generated using UCSC HG38. I realized that is a zero-based coordinate system.
I annotated the vcf with VEP and I also got to know that Ensemble uses a [one-based …
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### Updated: September 30
* (p.2) Added a table that compares the functional and imperative programming.
* (p.12) "Boolean expressions _~are~can_ be combined by boolean operators:"
* (p.17) Added t…
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Question from user:
Based on sequence ontology stop_gained is a feature_truncation and inframe_insertion is a feature_elognation, could stop_gained and inframe_insertion be together?
o for example, …
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### Need
As a clinician interpreting cases with a significant risk of equal presence of somatic variants in the matched normal, I want the ability to adjust the somatic in normal frequency when doi…
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Hi!
I used the following command to run the VarGen pipeline but I am getting the following error:
```
> disease_variants disease_annotation