Exomiser - Genome DB Build

This is a Spring Boot CLI application and as such has one idiosyncrasy which will prevent a build from launching, if not set in the application.properties.

The absolute requirement for anything, even --help to work is for the --build-dir variable to be set and this must be set using an equals sign i.e.

$ java -jar exomiser-data-genome-${project.version}.jar --build-dir=. --help

By default, this is set in the application.properties to . i.e. the current working directory but can be overriden.

Also, note that the --assembly and --version must come before any other arguments in order that they are correctly set for use with other optional arguments.

Build transcript databases and build/annotate ClinVar data. The ClinVar data build now requires a transcript database so that the variants can be annotated for gene symbol and variant effect to be in line with the output from Exomiser. Whilst these are available in the MC field of the ClinVar VCF file, the effects are not sorted according to reference transcript order, so in cases where more than one transcript overlaps a variant, the most damaging effect is reported first, even if the MANE/MANE_Clinical or canonical transcript has a less damaging effect.

$ java -jar exomiser-data-genome-${project.version}.jar --assembly hg38 --version 2311 --transcripts ensembl --clinvar

Will create an output directory 2311_hg38 containing the files:

2311_hg38/
├── 2311_hg38_clinvar.mv.db
└── 2311_hg38_transcripts_ensembl.ser

Create a new ClinVar database from the latest ClinVar release using an existing Exomiser release, in this case 2309_hg38:

$ java -jar exomiser-data-genome-${project.version}.jar --assembly hg38 --version 231112 --clinvar /data/exomiser/2309_hg38/2309_hg38_transcripts_ensembl.ser

Will just create the ClinVar database, annotated using the specified transcript data:

231112_hg38/
└── 231112_hg38_clinvar.mv.db

n.b here the ClinVar data has been created for the 20231112 release, so it is possible to update the clinvar data for Exomiser on a weekly basis to keep up with ClinVar