genotype score for genes with lots of called pathogenic variants

TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities

https://thejacksonlaboratory.github.io/LIRICAL/stable

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genotype score for genes with lots of called pathogenic variants #95

Closed pnrobinson closed 5 years ago

pnrobinson commented 5 years ago

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 new heuristic essentially assumes that if we observe more than 2 variants (one for autosomal dominant) theny they are all background. It will fix the problem we saw today

pnrobinson commented 5 years ago

done. Still needs testing. @julesjacobsen This should solve the issue where multiple pathogenic calls are made (irregardless of the quality actually)