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Write a script to apply the user's filter selections to an annotated VCF.
Input parameters:
- _Filters_: command-line arguments describing the user's filter selections, e.g. "filters=clinsig:patho…
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## Describe the issue
When running VEP using a local implementation via Docker, we see that variants are annotated with different ClinVar clinical significance values depending on the corresponding t…
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Hi,
Is there a way to include variants in RNA genes without getting all non-coding variants in regular protein-coding genes (or intronic variants in protein-coding genes that are also ncRNA variant…
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# Tasks
## Difficulty: low
- [x] Determine why certain genes / diseases are missing
- [x] Omit 'Recurrent Neisserial infections' as a node in the network plot (since everything connects to it in t…
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If the ClinVar significance contains a term `Pathogenic,drug_response`, does gene.iobio remove the non-significance terms (drug_response in this case) so that the displayed term is just `Pathogenic`? …
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We moved to rankscore, but raw scores are used in ACMGv4 in PP3_supporting
Check out if any others are used
We should also run eg REVEL as a tool instead of dbNSFP
If not on the short variants then…
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On the page for Marfan syndrome, there are 1577 variants. Many of them are from dbSNP, including this one , which has no known clinical significance.
https://www.ncbi.nlm.nih.gov/snp/rs2017765?ve…
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# nf-core/sarek feature request
## Is your feature request related to a problem? Please describe
Typical effect prediction (SNPEff, VEP) will not take into consideration variants "in phase", i.e…
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Related to #35.
In order to include only conflicting variants where at least one submission is pathogenic / likely pathogenic, the individual submissions data is needed. That is not present in the …
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**Background**:
- [Genome Nexus](https://www.genomenexus.org/) is a comprehensive resource integrating variant annotations from more than a dozen sources relevant to cancer. The annotations can be a…