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Go to MUC3A from Nebula. There are loads of missense variants, but trying to save them fails.
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## Describe the issue
It appears that the 1000G "AF" field is sometimes not populated even if the subpopulations (eg. AFR_AF, AMR_AF etc) are populated with high frequencies.
## Additional inf…
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converting CSQ to a usable object via the js expressions would be useful. the most useful part of this is the missense/gene impact stuff which is provided by bcftools CSQ. If that has an API, it would…
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I'm trying to filter for VEP plug-in splice prediction annotations in the INFO field, by e.g.
```
--info "INFO.SpliceAI_pred_DS_AG >= 0.5"
```
and I get error
```
[slivar] error evaluating inf…
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## Describe the issue
Hello everyone, I am using VEP docker. I am able to annotate my vcf, but it fails to annotate rs identifiers (I understood they are within cache). I manually downloaded cache an…
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## Describe the issue
When running VEP this message appears:
`Use of uninitialized value in subtraction (-) at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/TranscriptMapper.pm line 384, line 1.`
The o…
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Hi,
We noticed that we see no **transcriptIds, mainTranscriptId, gene_ids** calculated in the pipeline (luigi pipeline) for some variants. These annotations depend upon **sorted_transcript_conseque…
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https://www.biostars.org/p/9474428/#9474883
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Dear GSvar team,
by my last issue, I got the installation of the megSAP on a ubuntu docker to finish without errors.
My main goal to use megSAP is to annotate an input vcf file using vep and th…
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## Describe the issue
Following from my closed issue: https://github.com/Ensembl/ensembl-vep/issues/1007
I've now been able to achieve annotation of all of the columns I require, but there is stil…