damiansm

SpliceAI

8

https://github.com/Illumina/SpliceAI

SQUIRLS

1

- Peter's team is implementing an algorithm to detect exonic splicing enhancer mutations. I think we can try to do that, cryptic splicing, and MaxEnt analysis of the entire canonical...

Incorporate genic intolerance scores

2

Sources of data ** New: ExAC paper scores and mouse emb lethal info into Exomiser: 79% of loss-of-function-intolerant genes to have no known associated disease (~2500): list of the loss-of-function-intolerant...

Virtual gene panels

2

We already have the ability to filter by a list of genes (virtual gene panel) which is great but not exactly what we want as ideally we want to also...

Allow trio input as separate VCF files / add tutorial on creating multi-sample VCF.

7

Should we allow the ability to upload patient and parent exomes as 3 separate VCF files rather than a multi-sample. Or is it easy enough for people to use vcf_merge?

Transcript annotation

3

Would be good to highlight the canonical transcripts, Gencode_basic transcripts etc in the output so users can check the maximally damaging Jannovar consequence belongs to a clinically relevant transcript as...

GTEX expression filtering/prioritisation

1

* with Lukas from Jenny Taylor's team, 3rd yr PhD * Has method to generate an expression score for each variant based on how similar the expression of the gene...

Nico is working on a Jenkins pipeline to generate the hp-hp, hp-mp etc mapping flatfiles for Exomiser and other Monarch applications See https://github.com/monarch-ebi-dev/monarch_ontology_data, especially the Makefile Waiting on Jenkins memory...

Improved allele frequency filtering and incomplete penetrance

2

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...

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...