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I've checked a few and I think I see a pattern. Looks like only the clinical significance is parsed correctly.
To test this:
- on stage or prod, take one RD case and one cancer case
- Go the the …
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* pvactools version: 1.3.3
* Python version: 3.5
* Operating System: linux
**Describe the bug**
A clear and concise description of what the bug is.
I use a different reference genome for al…
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Hi,
I tried to use INFO.impactful with an adjusted list of variants on VEP/CSQ annotations . And I got an error:
> [slivar] warning! no IMPACTFUL_CUTOFF specified. INFO.impactful will not be us…
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gtiao updated
3 years ago
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## Describe the issue
When using a custom dataset for annotation of Genome data (Even Clinvar), vep throws segmentation fault error. Annotation works if I use data from cache, i.e. when using ```--ev…
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I have noticed that `bcftools csq` will not assign any `BCSQ` field for intergenic variants.
When used with `bcftools +split-vep` this causes all intergenic sites to be dropped due to the following…
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Hi,
Source column is empty in results. In the old version it came as refseq or ensembl so I could filter my results, but in this version it only comes with "-".
### System
- VEP version: [103…
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Following code for launching MoPepGen:
```
sudo docker run -it --rm -v /data/ref/GRCh38/ref_star/:/genome/ -v /data/resources/proteomics/hsapiens/GENCODE/GRCh38.13/release_34/:/proteome/ -v /data/…
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```
gemini annotate -f exome.vt.vep.vcf.gz -o list -e AF -t float exome.vt.vep.db
updated 100000 variants
Non float value found in annotation file: 0.021,0.058
gemini query -q 'select variant_id,AF f…
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When importing a VEP annotation VCF, we should read the file's meta data and verify that the VEP version is as we expect (or die loudly)