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Our initial ingest of ClinVar (see #7) used a tsv file that was missing much of the data only captured in their XML dumps. Our second pass will leverage the XML data, and include full evidence and pr…
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Hi,
Thanks for providing this tool and source code. The output looks great!
Is the license for this software open? If so, any guidance on the modifying the software to generate a summary of gener…
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The ACMG guidelines argue against use of the terms "mutation" and polymorphism. To be more consistent with these guidelines we could rename our `Variant Origin` values as follows:
Somatic mutation…
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Assertions endpoints are now implemented on the server, and need to be added to the UI as first-class entities.
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Two things that are somewhat urgent:
1. I am trying to edit the list of ACMG evidence codes for an assertion:
https://civic.genome.wustl.edu/events/assertions/4/edit/basic
I am getting an error …
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https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf
Someone please work on this independently. The script should be working independently disregard to wha…
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based on: https://gatkforums.broadinstitute.org/gatk/discussion/8815/oncotator-variant-classification-and-secondary-variant-classification
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Since modified values were added to criteria, there are cases not covered in ACMG Guidelines 2015, e.g. case 2 PVS (very strong) and case 2 BA (stand alone). Right now, such cases result assertion "Un…
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Currently we use `Positive` and `Negative` for `Clinical Significance` values but it would make more sense to use the nomenclature from the ACMG guidelines for `Predictive` evidence:
https://www.ac…
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Found this in VarInterp274, looks like a mistake to me
```
"condition": [
{
"cg:id": "-"
}
],
```