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Can civicbot revise evidence direction and clinical significance for all predisposing evidence to NA?
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Use case from the VHL project. A group reports on 10 patients with VHL variants. A year later the same 10 patients plus 3 more appear in an update paper. There are some additional details on the sa…
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I found that the swifter groupby apply chain will encounter the error when trying to sort index, if I set dropna to False for the groupby step.
Here is the error log:
`
Traceback (most recent cal…
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The ClinVar whitelist option (default = true) will set all P/LP 2*+ variants found in a VCF file to have a score of 1.0.
The issue with this is that, while it works well for pathogenic variants, it…
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Using GATK jar /usr/local/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_writ…
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Several predictors have been recommended/requested to be added to the VCI Variant Type predictors table, additionally the predictor table should be updated to be in line with Pejaver et al 2022 and St…
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**Background**
Currently there are 21+ gene-specific modifications of the ACMG guidelines that should be consulted when curating to determine gene-specific thresholds for each criterion. For example, …
sksmi updated
3 years ago
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This repo currently tracks both:
1. Data model definitions for the DSPCore and extensions, in `.ttl`
2. Jade schema definitions roughly mapping to the data model, in JSON
The more I think about i…
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Currently an endpoint for retrieving annotations for an individual case is already exposed in the following endpoint:
https://github.com/bihealth/varfish-server/blob/1e956c92aabfc7fee9caaefaec60f00…
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Starting a new ticket specifically dedicated to the question of whether to lump or split representation of Variant Pathogenicity and Variant Oncogenicity Statement types.
This discussion was start…