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I'm experiencing the issue with the `tabix `indexing of `AlphaMissense_hg38.tsv.gz` file.
I've installed alphamissense plugin in VEP and have downloaded the requested files and launch the tabix comma…
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I am getting the following error from the gtf library when trying to annotate my vcf with stringtie output.
```
$ vcf-expression-annotator -o /shared_dir/temp.annotated.vcf -s sample /shared_dir/tem…
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Hi team
Thanks for the great toolkit. I was wondering if this could be updated to work with later Ensembl vep releases (the latest as of Feb 2023 is 109.3 - https://github.com/Ensembl/ensembl-vep/r…
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I need to annotate some indels for chromosome 22, and then scale this step to the full human genome. I'm running vep locally using snakemake in a HPC environment with 75Gb of RAM. The input file has ~…
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I am an enthusiast of this whole concept of BioContainers, and yet very new to it (and dockers as well). So, this issue might likely be because I am missing something.
When I try to to run the comman…
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Currently we have [--check_ref](http://ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_check_ref) enabled when running VEP. This generates a list of reference mismatches if the VEP cache u…
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The following gist: https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697
seems to only work for linux systems. Is there an equivalent one for Mac OS? Also, does vcf2maf only work for VEP…
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Now that we have a new endpoint with version of VEP etc, it would be nice to add this information in the MAF header. That is include versions for:
- Genome Nexus Server
- Genome Nexus Seed Databas…
inodb updated
2 years ago
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I want to use gemini to annotate my variants generated from GATK pipeline using hg38 genome. Below is the gemini version I'm using:
iit@iit:~$ /home/iit/bin/gemini -v
gemini 0.30.2
Installation:
…
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While updating the continental extension bookmark (see attached PRM), I found that switching between using continuous and discontinuous compositional fields (`set Use discontinuous composition discret…