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When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule ann…
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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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Given that VEP is a tool for annotating variants with transcript-level data, I struggle to think of a scenario in which you *wouldn't* want the dbNSFP annotations to be properly split out and matched …
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View details in Rollbar: [https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5326](https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5326)
```
Traceback (most recent call last):
…
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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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- build mehari transcript DB (ensembl):
- download cdot for ensembl and grch37 / grch38
- download ensembl FASTA for transcripts
- create / fill seqrepo with ENSEMBL FASTAs
- build…
tedil updated
3 months ago
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### Description of the bug
This bug has been around for a while now. When Sarek encounters an error is will often issue the correct error message along with a couple of wrong error messages. The wron…
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Use build 38.
Add ExAC annotation allele frequencies:
/cluster/project8/vyp/AdamLevine/annotations/ExAC/0.3/ExAC.r0.3.sites.vep.vcf.gz
Have a look at this script to prepare allele frequency from INFO…
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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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Module 4 VEP annotation from Esembl
gl186 updated
7 months ago