Improved allele frequency filtering and incomplete penetrance

exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants

https://exomiser.readthedocs.io

GNU Affero General Public License v3.0

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Improved allele frequency filtering and incomplete penetrance #352

Open damiansm opened 5 years ago

damiansm commented 5 years ago

We could consider using the approaches described in https://www.nature.com/articles/gim201726 and exposed in the tool at http://cardiodb.org/allelefrequencyapp/ to calculated an expected MAF cutoff based on mode of inheritance, penetrance, disease prevalence and heterogeneity. Prevalence levels are available from Orphanet now or we could just a let a user enter the values and set MAF filters appropriately.

damiansm commented 1 month ago

See recent Carloline Wright papers. Look at gel diagnoses and P/LP and segregation to see how often happening. Want a more nuanced model rather than just 0% or 100% as we have now.

damiansm commented 1 month ago

Increased diversity: can we get access to H3 Africa genomes etc.