Jules Jacobsen

Users want to use Exomiser as an annotation tool...

1

There are at least [one](https://github.com/exomiser/Exomiser/issues/496#issue-1744349471), [two](https://github.com/exomiser/Exomiser/issues/488#issue-1645683287), some (private communication), [lots](https://github.com/exomiser/Exomiser/issues/258#issuecomment-383484527) of cases where people are using Exomiser as an annotation tool rather than a prioritisation tool. Do we make this...

Add analysis strategies to docs

1

There are probably too many confusing example input files in the cli examples directory which leads to people rolling their own sub-optimal analysis steps. Getting the best from Exomiser should...

The module provides IO for phenopackets of both versions and all data formats (JSON, protobuf, YAML). Use this to parse the input sample for analysis.

`OmimProritiser` is a special case `Prioritiser` which needs to be worked around in many places due to the fact it serves dual purposes which are better split into separate concerns.

Add module-info.java in `org.obographs` namespace

1

We need to start migrating obographs to enable more modern java applications to fully embrace the benefits of the module system. See the Java tutorial: https://dev.java/learn/modules/intro/ > Regarding module name...

Pedigree

3

Adding schema definition and docs for implementation of the [GA4GH Pedigree Standard](https://github.com/GA4GH-Pedigree-Standard/pedigree)

Use TermInfo instead of multiple strings in similarity.yaml

8

There are a lot of string fields using field names to group them into entities which would likely be better as `TermInfo` types. e.g. ```yaml classes: PairwiseSimilarity: abstract: true description:...

Do we need to expose the `temperature` field?

4

https://github.com/monarch-initiative/ontogpt/blob/8bb0dc058794924871f5b948fd851b9ed4694d4b/src/ontogpt/clients/openai_client.py#L50-L67C1 According to [the OpenAI best practices for prompt engineering](https://help.openai.com/en/articles/6654000-best-practices-for-prompt-engineering-with-openai-api): > **`temperature`** - A measure of how often the model outputs a less likely token. The higher the temperature, the...

Incorrect InheritanceMode calculation for multisample VCF with multiple alleles.

5

Consider the following: ``` ##fileformat=VCFv4.2 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Cain Adam Eva Abel 1 145513533 . T C,A 123.15 PASS GENE=RBM8A GT:DP 1/2:21 0/1:33...