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These are tasks to refine the filtered event table based on feedback from Marcin:
Responsibilities:
Clean-up and aesthetics:
@xanthopoulakis will work on the following:
1. Column order for the…
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Hi,
I would like to report an issue with the variant annotation in VEP version 113. Specifically, variants that should be annotated as `frameshift_variant` are being incorrectly annotated as `infra…
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## Describe the issue
Some BND variants are missing vep annotations, while the rest have them.
## Additional information
### System
- VEP version: 113
- VEP Cache version: 113
### Full VEP…
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## Describe the issue
I'm annotating a vcf coming from Manta. In the output, some of the variants are not annotated and I don't know why. In my vcf, all the variants have all fields information (incl…
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Hi,
I observed that for the variant **1:98348885_G>A**, the HGVSp annotation returned by VEP is **p.C29=**. However, the expected annotation should be **p.R29C**.
This discrepancy might lead to conf…
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**Describe the bug**
Currently, mehari does not annotate tx on the MT chromosome.
```
curl 'http://mehari:8080/seqvars/csq?genome_release=grch37&chromosome=MT&position=73&reference=A&alternati…
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## Describe the issue
A variant (X:15823107C>CAGCCGG) was not annotated using the gnomADe VCF provided (r2.1.1) by VEP b38. The gnomADe VCF has this variant present with AF=0.0147404 and so should ha…
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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.**
Some variant calls might be incorrect or need to be adjusted to take multinucleotide variants into account. Currently the user might…
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I appreciate this valuable protocol, and it has been beneficial for me. I have some questions, and I would be very grateful if you could guide me:
- Some of the links you provided to download the …