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We had some discussion in the @Clinical-Genomics/rare-disease team and we find the filename `managed_variants.vcf` to be somewhat confusing. The file name is ambiguous as it is not clear whether thes…
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Hi,
I'm querying the API as instructed in the tutorial notebook.
```
httpClient = client.HttpClient("https://brcaexchange.org/backend/data/ga4gh/v0.6.0a7/")
query = httpClient.search_varian…
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It has been requested several times to be able to group gene databases together under a group or LSDB, within one LOVD3 instance. This is particularly useful for LOVD2 databases that used to have thei…
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Hello ctat team,
I am trying CTAT v3.2.0.
After I run it, there were ~.vcf.gz and ~.XGBoost-classifier.vcf.gz.
I think the raw GATK result is ~.vcf.gz
(If I am looking for the variants from the…
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Compare
- http://www.informatics.jax.org/allele/MGI:3894845
- http://beta.monarchinitiative.org/gene/MGI:3894845
- requires linked xref to MGI
- type "gene trapped allele"
- etc
May require loa…
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### Summary
Create a unified data model for disease knowledge. There is a wealth of information that can be associated with any disease: what phenotypes are manifested, the causative variants and t…
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Tagging required in both GCI and VCI... parallel implementation.
Tag use cases:
1. Alerts (e.g. new publication, new ClinVar entry, time for re-evaluation, etc) Auto-tags added by VCI
-…
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Hi Sigve
Thanks for another awesome framework. We (@umccr) are very much interested to incorporate this into our reporting.
I have looked at the github repo/code and tested it locally - it works…
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Clinical Significance should mention the new Oncogenic evidence type
>Positive or negative association of the Variant with predictive, prognostic, diagnostic, or predisposing evidence types. If the v…
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Good luck!
Requirements
```sh
apt install \
libdbi-perl \
libdbd-mysql-perl \
curl \
zip \
build-essential \
zlib1g-dev \
libmodule-build-perl \
git
```