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This a duplicate of #279 that I couldn't reopen.
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.8
- OS name and version (`lsb_release -ds`): ubuntu20.04 docker container
**To Reproduce**
Exact bcbio command you hav…
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Hey,
I am new to SnpEff and not sure what this is causing. I experience some problems when downloading a database via the `download` option. I am running:
```
java -jar snpEff.jar download GRCh…
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I noticed the following problem. I use
SnpEff 5.0 (build 2020-08-09 21:23)
I run the command
java -jar snpEff.jar -i vcf -o vcf -fastaProt out.fa hg38 in.vcf > out.vcf
Now look in the file out.fa …
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Hi there,
I have ran VEP for covid-19 using
1) a gff file
2) genome reference file
3) variation file of ensembl format
and I get back a very poor variation annotation.
Is it something t…
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(extracted from another issue)
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Sarah:
add an annotation column (for example: intronic; exonic-nonsynonymous; exonic-splice; exonic-synonynmous; intergenic; 5' UTR; 3' UTR)
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Peter:
1. …
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Hi folks,
I am using snpEff to annotate variants called from hg19 aligned short reads. I am relying heavily on the impact/effect information that is reported. One recent task I've been tackling…
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I'm using bcftools analysing each chromosome block. However, there're some 0s in transition and transversion within each block. So I wonder how does the bcf_tools deal with those samples with 0 transi…
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Hi,
I recently installed the snpEff v5.0.0, and when I tried to download the Arabidopsis thaliana database using
`$java -jar snpEff.jar download -v Arabidopsis_thaliana`
the error message sh…
chc36 updated
3 years ago
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We need modules in [nf-core/modules](https://github.com/nf-core/modules) for:
Please tick a module if you are working on one, and add the link to the PR once you created it
- [ ] allelecounter
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