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Hello,
I have been playing around with the rvtests docker container for a couple of days and things have been running smoothly, thanks for the nice utility!
Yesterday I attempted using a VCF fil…
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Hello, I would just like to know if this tool works for snpeff outputs where the rows have multiple annotations?
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There are toolshed identifiers inside Galaxy workflows, but these are not carried forward into the RO-Crate nor to the knowledge graph.
Example, from https://workflowhub.eu/workflows/7 we have `Gen…
stain updated
3 months ago
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Hi,
I am trying to run the tool with a vcf file annotated with the latest SnpEff, which does not include descriptions, instead the annotations are of the form:
ANN=A|intron_variant|MODIFIER|LOC10028…
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## Sept 26, 2024
@natefoo started the process:
- Galaxy dbKeys will be set to GenBank or RefSeq IDs (`assembly version ID` column in https://brc-analytics.org/data/organisms)
- Names (in tool dropdo…
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Dieter Best shared an example VCF annotated with snpEff with me on Google Drive. This will be used to explore whether it is possible to use this annotation format to make pVACseq predictions.
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**Describe the bug**
SNPEFF_ANN fails due to SnpEff being unable to read the config file (snpEff.config). I believe this is because it is being passed in the $args, rather than as an input, so the fi…
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### Description of the bug
Singularity container retrieval failed when trying to download the nf-core/sarek pipeline. While making image from oci registry I got an error fetching image to cache and f…
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I tried to run snippy with the following genbank file:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/632/635/GCF_008632635.1_ASM863263v1/GCF_008632635.1_ASM863263v1_genomic.gbff.gz
However, the p…
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Support ANN fields name .
See :
http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf
dridk updated
7 years ago