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The link currently goes to v3 in GRCh38
SAP have also asked for this to be patched back
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Hi
We're very pleased with vcfanno performance but we found some modifications in the final vcf that annoys us a little.
Basically, vcfanno rounds out "QUAL" to 1 decimal point (from 2 in the origin…
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Hello everyone,
I am running the annotation step using VEP with the "dbNSFP" plugin. I tried running dbNSFP with `ALL` filters and specified the parameters I needed, but I am not seeing all the plu…
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Hi,
Any plans to update the gnomad frequencies to v4 (https://gnomad.broadinstitute.org/news/2023-11-v4-structural-variants)?
Regards,
Prasun
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We are still using 3.1 for GRCh38, haven't generated one for new gnomAD 4
Code currently dies looking for this version, which means installing from scratch no longer works
Need to create a v4 GRCh38…
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## Feature request
### Module(s) or script(s) involved
AnnotateVcf Module
### Description
Could we please add gnomAD allele counts in addition to the gnomad allele frequency?
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**Description**: open more genes that span the inversion
**Error message**: Cannot read properties of undefined (reading 'genes')
**Stack trace**:
```
TypeError: Cannot read properties of unde…
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When running this command
Rscript workflow/scripts/preprocess.R -i gnomad_extracted.csv.gz -o gnomad_extracted_prepro.csv.gz
I got this error message: Error in str_split(n_occur[n_occur$Freq > 1,…
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Sub-ticket for gnomAD v4 update #47
The goal of this ticket is to do the "like for like" update of the VCI population tab from gnomAD v2 to v4 data, along with deprecating a few sections of the po…
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The issue I'm encountering is that when running the following vep command line:
`vep --cache 112 --dir_cache /media/user/Maxtor/SV_Analysis/outputs/vep_output/vep_caches/homo_sapiens/homo_sapiens_m…