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Hello, perhaps an obvious question, but I wanted to verify.
Is the included file "uORF_5UTR_GRCh38_PUBLIC.txt" the same as the "uORF_starts_ends_GRCh38_PUBLIC.txt" mentioned in the documentation?
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bwubb updated
2 weeks ago
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Hi there!
In the manuscript, you mentioned that "VEP (version 102.0) was used to annotate variants generated by dipcall when aligning the T2T-CHM13 reference genome (chm13_v1.0_plus38Y.fa) to the …
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Can we also support IDs under annotation-controller?
- [x] `/annotation/dbsnp/[dbsnp_id]`
- [ ] `/annotation/cosmic/[cosmic_id]`
- [ ] `/annotation/hgmd/[hgmd_id]`
We can utilize the following…
jjgao updated
6 years ago
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For each VEP gene hit, collect the associated GO terms and generate a table with the fields cultivar, snp, gene, go terms, and any other interesting annotations from VEP.
Could use the GO VEP plugi…
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A CCB researcher emailed about how 17:7574012 G>A has HGVS of ENST00000269305.4:c.1015G>T
As it's -'ve strand you'd think given the ref G would be complement C ie HGVS should be ENST00000269305.4:c.…
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VEP 111 forwards requires positional arguments in the construction of the custom annotation fields which will not work with out current config and app set up.
example from their docs:
```shell
./…
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## Describe the issue
We investigated how vep annotates inversions and performed an inversion in the vcf file on the region chr17:7671525-7685229, where vep was expected to assign a HIGH impact to th…
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## Describe the issue
Coordinates for insertions relative to the reference should be as documented here: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#input :
"An insertion (of any …
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### Description of the bug
After the recent update of the module [bea3ca9](https://github.com/nf-core/modules/commit/bea3ca998816a7f812b1bbbcb27c3a9ffbac0706), `ENSEMBLVEP` process fails:
```
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Hi,
I've put into a separate assets data needed to run germline analysis for Homo sapiens here : ~~https://github.com/apraga/human_genome_assets~~ https://github.com/apraga/germline-analysis-vep
D…