Exomiser
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Make sure diseases in the omit-list.txt are excluded from the db build
HPO team have a curated set of OMIM disease IDs with gene associations they suggest omitting as they are susceptibility genes etc
Investigation revealed there are some 138 diseases in the https://github.com/monarch-initiative/hpo-annotation-data/blob/master/rare-diseases/annotated/omit-list.txt file that are included in phenotype-annotation.tab and, hence, our database.
Easiest solution will to be to switch our db build to use http://compbio.charite.de/jenkins/job/hpo.annotations.2018/lastSuccessfulBuild/artifact/misc_2018/phenotype.hpoa and this already has them excluded