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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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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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For discussion:
# Specification: VCF to VRS Processing Package with Cohort Allele Frequency Generation
## Overview
This package processes Variant Call Format (VCF) files to ensure compatibility…
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## Describe the issue
After performing variant calling with GATK's HaplotypeCaller and normalize multiallelic sites usign bcftools, I annotate my variants usign Ensembl VEP v113.2. There seems to be …
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Vcflib `vcfbreakmulti` doesn't handle annotations correctly during splitting
- [x] create megSAP test for this error (e.g. calling on the extracted region of DNA2106177 shown below)
- [x] test if …
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Hi. I'm trying to use [erased annotations](https://agda.readthedocs.io/en/v2.7.0.1/language/runtime-irrelevance.html) but as I can see agda stdlib doesn't really support them. What I stumbled upon so …
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Hi, thanks for sharing this library. Good to see some tooling around JTE and HTMX. :)
I've upgraded to 3.6.1 and tried to migrate to the new recommended approach, which is using `HtmxView` as a res…
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The following annotations would be really useful for the non-redundant variants:
- overlap with genes
- repeat regions and segmental duplication regions
- overlap with known dosage sensitive gene…
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### Current Behavior
There may be discrepancies between the annotations generated by the Variant-Linker tool and the VEP online version.
### Proposed Solution
- Select a set of representative…