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**Describe the bug**
Run ends with error due to a missing scipy import. I'm running a WGS trio from Illumina DRAGEN pipeline through Cravat with ClinVar, case-control, and SpliceAI modules.
**To …
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Dear Chengyao,
Is there any script shared in this package to preprocess ClinVar data?
Thanks
Shicheng
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Hello
I was wondering if you think there is any value in updating the MITOMAP and ClinVar annotation files? From the README it looks like the last updates were in 2015.
Thank so much
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Something like the pubmed existence check endpoint, where we hit their api and then return the variant name if found
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* Generate 100/1k/10k random HGVS from ClinVar
* Install SeqRepo locally
* Benchmark how long it takes with JSON and REST client - check out caching/non caching etc
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Transpose table to list all possible transcripts and then indicate whether one is MANE select/clinical. See ClinVar result table for inspiration.
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Right now, we are using e.g. https://myvariant.info/v1/variant/chr10:g.89623200C%3EA?fields=clinvar.rcv.clinical_significance&dotfield=true
To retrieve data on the fly. This is slow and ideally we sh…
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Given an RDD of Association objects, trying to add annotations from the ClinVar database providing biological context for these variations.
Annotations will include information about how variant ma…
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This includes the ability for the VCI to automatically update any previous ClinVar submitted Variant Interpretations with the ClinVar SCV id and url as soon as the data is published in ClinVar. This w…
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As a user, I would like to be able to sort the Clinvar widget data by `review status` and `clinical significance`.
At the moment, the ClinVar widget is not sortable by any of the columns/fields.
Als…