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Add the annotation of called variants with SNPEff.
This will require either the creation of a local SNPEff database, or the use of reference sequences that are already included.
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Hello @jodyphelan,
We are currently implementing the analysis of IS6110 insertions onto our structural variants workflow, but we are running into some unexpected TBProfiler outputs.
The attache…
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I am trying to annotate variants with dbNSFP using VCFs of individual chromosomes, that have already been annotated with SnpEff and with gnomAD exome frequencies using SnpSift. I am able to do this fo…
ji575 updated
2 years ago
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Thanks for the nice software! Hopefully this is not duplicated. I got this error when trying to run snippy, installed with mamba, on a gbk reference.
```
WARNING_GENE_NOT_FOUND: Too many 'WARNING_…
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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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Hello,
Is it the intention of `--vcf_info_field ANN` to adhere to the VCF ANN specification? While some fields do match, there are several that do not, and more troublesome for consumers some that…
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Came up at the 2020 Elixir biohackathon.
Experimented with this in https://github.com/ResearchObject/ro-crate-py/tree/gxformat2_cwl_conv. [Here are the changes](https://github.com/ResearchObject/ro…
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### Hi Strelka2 Team,
I am using the release `strelka-2.9.10`
After running strelka in a somatic way for whole genome, we tried to annotate the strelka's vcf with snpEff; That tool (snpEff) show…
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Link to the tutorial is below. Under the sub-heading "Identifying Candidate Mutations: Variant annotation." The version of the SnpEff tool required for the Hand-on is 4.1.0. I tried my hands on the tu…
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### Is your feature request related to a problem? Please describe
- [x] bedtools/merge
- [x] bedtools/sort
- [x] cat/fastq
- [x] custom/dumpsoftwareversions
- [x] ensemblvep/vep
- [x] fastqc
- [x] ga…