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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 …
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When I try to annotate the results with VEP I get:
```
WARNING: variant 259 on line 280 is too long to annotate: (78162751)
WARNING: variant 260 on line 281 is too long to annotate: (78180620)
W…
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## Describe the issue
Hi, this is not a specific problem with VEP tool but more understanding issue.
I have a variant in PTEN with HGVSc: NM_000314.8:c.634+5G>C which annotated via VEP command line …
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## Unable to write to volumes when running on github build agents
When running VEP within a docker container upon a github build agent I was unable to write output files to the mounted volume.
M…
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- [x] Don't use bare numbers in your code. Write a generic function that extracts a component based on some settings (e.g. 'by specifying N or P and the time point (100) and some window before and aft…
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We haven't looked at the annotation pipeline going into gene for a long time and it would be worth revisiting. For example, we are using vt to normalize and decompose, but we can likely achieve the sa…
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As discussed with @buniello and @DSuveges, we want to create a new column in the variant index named `description`. This column would be equivalent to the field we have for other entities, containing …
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## Describe the issue
For below variant:
`#CHROM POS ID REF ALT QUAL FILTER INFO`
`chr21 5233678 . A AATTT . . .`
In VEP 109.3, this variant has HGVS notation: ENST00000623753.1:n.132-758_132…
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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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Tnscope, and perhaps other variantcallers create wierd multi-allelic insertions. These variants get gnomad frequencies per allele separated by "&" which coyote cannot handle. For these rare occasions …