GenomesDB configuration

This file is responsible for configuring which reference genomes and gene models are available to the GPF system and which it should use by default.

Example Configuration

defaultGenome = GATK_ResourceBundle_5777_b37_phiX174

chrAllFile = %(wd)s/genomes/GATK_ResourceBundle_5777_b37_phiX174/chrAll.fa

defaultGeneModel = RefSeq2013

geneModel.RefSeq2013.file = %(wd)s/genomes/GATK_ResourceBundle_5777_b37_phiX174/refGene-201309.gz
geneModel.RefSeq.file = %(wd)s/genomes/GATK_ResourceBundle_5777_b37_phiX174/refGene-20190211.gz
geneModel.CCDS.file = %(wd)s/genomes/GATK_ResourceBundle_5777_b37_phiX174/ccds-201309.gz
geneModel.knownGene.file = %(wd)s/genomes/GATK_ResourceBundle_5777_b37_phiX174/knownGene-201309.gz
geneModel.RefSeqMito.file = %(wd)s/genomes/GATK_ResourceBundle_5777_b37_phiX174/refGeneMito-201309.gz

regions.X = X:60001-2699520,X:154931044-155260560
regions.Y = Y:10001-2649520,Y:59034050-59363566



defaultGenome = <default genome id>

The default genome to use. The genome id must reference a configured genome from one of the [genome.<genome id>] sections below.

[genome.<genome id>]

This section contains information about a single genome.


chrAllFile = <>


defaultGeneModel = <default gene model id>

The default gene model to use. This id must reference a defined gene model from one of the geneModel.<gene model id>.file properties below.

geneModel.<gene model id>.file

geneModel.<gene model id>.file = <gene model filename>

This property defines a gene model. It sets both the id of the gene model and the absolute path to its file. The id can be chosen by the user.



regions.<> = <comma separated >