-
Hello there,
My file was annotated using VEP, and I am trying to convert the annotated VEP output to a format accepted by VPOT.py using these commands:
python3 ../VPOT_6_1_convertVEP.py utility …
-
## Describe the issue
I encountered the same problem as shown in the figure when using the DownStream plugin (there is no such problem when using --hgvs). Following these three instructions, I update…
-
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):
…
-
Hi,
I tested using version 113 of VEP. Small VCF files work fine, but when I provide a larger VCF file with about 100,000 lines, the program is interrupted, showing numerous warnings: WARNING: “Trans…
-
I noticed that VEP 112 predicts an opposite consequence as compared to previous versions for certain insertions (rare cases). It predicts `inframe_insertion,stop_retained_variant` in cases where `fram…
-
### Description of the bug
Adding this as a reminder that filter_vep can't filter on HGNC_ID in hg38, so I think no clinical set will be generated.
Should be [fixed](https://github.com/Ensembl/en…
-
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…
-
Good luck!
Requirements
```sh
apt install \
libdbi-perl \
libdbd-mysql-perl \
curl \
zip \
build-essential \
zlib1g-dev \
libmodule-build-perl \
git
```
-
Hi,
Thanks for developing this nice tool.
I'd like to use my own fasta and gff to annotate the VCF file, according to the mannual:
```
grep -v "#" data.gff | sort -k1,1 -k4,4n -k5,5n -t$'\t'…
-
- run with VEP `--most_severe`
- run AMS
- compare score