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iobio / gene.iobio

Gene.iobio vue
MIT License
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Refine logic for 'poor' and 'moderate' sequence quality on Variant inspect card. #912

Open tonydisera opened 1 year ago

tonydisera commented 1 year ago

It isn’t clear what the requirements for the “Sufficient depth and allele counts” are. If you change the settings for coverage, that doesn’t affect this
It works for me, but it is only looking at coverage min. It should look at coverage mean and median as well. It also has sloppy code (that’s on me) for setting ‘poor’ vs ‘moderate’.
var depthThreshold = {'good': self.cohortModel.filterModel.geneCoverageMin, 'moderate': self.cohortModel.filterModel.geneCoverageMin - 5};

var altRatioThreshold = { 'good': {'het': .1, 'hom': .6, 'homref': 0}, 'moderate': {'het': .05, 'hom': .4, 'homref': 0} };

AlistairNWard commented 1 year ago

Maybe we can include a tooltip on this section to indicate where you can change the settings