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http://bejerano.stanford.edu/mcap/
https://www.nature.com/articles/ng.3703
Method | Authors' Recommended Pathogenicity threshold | Misclassified known pathogenic variants
-- | -- | --
SIFT | <…
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If a variant has multiple clinsig values, for instance "Pathogenic/Likely pathogenic", it cannot be found using the CLINSIG-filter.
Multiple clinsig.values are stored in the database as a comma-sep…
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try this heuristic
```
if (number of observed path vars > 2) {
LR =Pois(#observed vars | lambda=2) / Pois(#observed vars | lambda=#observed vars)
} else {
-- use existing score
}
```
This ne…
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There are often cases where a known pathogenic variant my occur more frequently in a population than the frequency cutoff filter is set to.
Enable the ability to specify variants which should pass …
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>It is also important, in the introduction, and indeed for the presentation of information in the collated database, for the authors to be clear that the variant interpretation processes for germline …
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These terms has the same name and OMIM ID. Consider merge.
id: DOID:0080466
name: multiple congenital anomalies-hypotonia-seizures syndrome 2
id: DOID:0080139
name: multiple congenital anomali…
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When scores are publically available investigate performance - incorporates freq into score so woudl be a good replacement for us
One possibility would be to not incorporate freq into the default s…
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I've put some changes in for this which is now a lot more consistent in reporting ClinVar variant data. Previously it would only report it for non-synonymous, coding region variants, but now they will…
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## Bug Report
### Affected tool(s) or class(es)
`Mutect2` and `FilterMutectCalls`
### Affected version(s)
GATK 4.1.0.0 release (though I suspect this was also in 4.0.x)
### Description
M2…
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Hello:
When I run the Mastermind extension, it adds the comments to the output file in this way and does not add any mastermind information, but fills its columns with "-".
What is this error? How c…