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So everything has been working smoothly as far as alignment and variant calling up to this point, however, when I try to download the human snpeff database I get a make error. Here is the code:
gkn…
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"stop_gained" and "stop_lost" are valid SO terms. So is the SO term "start_lost". However, "start_gained" is not a valid SO term currently, despite start gains being possible in biology, and described…
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Was trying to run the workflow and encountered the following error:
```
['docker', 'pull', 'quay.io/snpeff:4.3']
Error response from daemon: error parsing HTTP 404 response body: invalid characte…
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installing fruit fly genome BDGP6 fails with missing snpEff download for bcbio_nextgen version 1.2.9
this url works: https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_BDGP6.28.99.zip
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This will remove the need for snpeff and particularly Java!
Docs: http://www.htslib.org/doc/bcftools.html#csq
Interface:https://github.com/samtools/bcftools/blob/develop/csq.c
Paper: https://…
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Using SnpEff to predict sequence variant to gene relationships produces predicate terms from the Sequence Ontology (SO). Currently biolink mappings for Sequence Ontology terms are incomplete. https://…
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### Description of feature
`snpEff ann` command has an option: `-canonList `, that can take in a tab-separated file containing gene and transcript.
> -canonList : Only use canonical tr…
YeHW updated
7 months ago
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snpEFF latest version lists canonical transcript first; the order of reported effects should not be re-ordered
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**Is your feature request related to a problem? Please describe.**
Currently it is not clear how mehari compares feature-wise to other available solutions.
**Describe the solution you'd like**
Id…
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