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## Describe the issue
A clear and concise description of what the bug is.
## Additional information
Please fill in the following sections to help us find the source of your issue as quickly as po…
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Thanks for your wonderful tool.
I've been trying to understand how to use capice to predict pathonicity of indels. I have two questions.
1. I don't know how to get a golden standard training d…
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**Describe the bug**
A user reported that filtering for "all clinvar pathogenic" variants does not work properly. We get both false positives and false negatives (pathogenic variants are not show…
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As of now, search can only be initiated by gene name/list or phenotype. If possible and practical to implement, I would appreciate a search feature that would pull up significant variants (i.e. anythi…
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Variants classified as [known pathogenic variants on MitoMap ](https://www.mitomap.org/foswiki/bin/view/MITOMAP/ConfirmedMutations) are being annotated as "likely benign" in the "MitoTip_interpretatio…
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Manuscript is accepted in principle, we just need to make these updates!
Reviewer 1:
- [x] 1.1 #1185
- [x] 1.2 #1185
- [x] 1.3 #1187
- [x] 1.4 #1185
- [x] 1.5 #1185
- [x] 1.6 #1191
Rev…
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Hi, I have succesfully run CharGer using the following command:
```
charger \
-f ~/vcf/17D2625146_FB_hg19.vcf \
-o test_charger_everything.tsv \
-l -D \
--mac-clinvar-tsv ~/clinv…
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We would like to include splice prediction as one of the facets when determining if a variant is plausibly relevant to diagnosis. This will be a little more complicated than just adding a new category…
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**Describe the bug**
A variant marked as one-star pathogenic in seqr, is actually benign per Clinvar. There are currently no records in Clinvar indicating it is pathogenic. It is possible the path en…
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**Is your feature request related to a problem? Please describe.**
Inclusion of mitochondrial variant calls from GS in seqr
**Describe the solution you'd like.**
Map created of features which wou…