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
[genomes]
defaultGenome = GATK_ResourceBundle_5777_b37_phiX174
[genome.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
[PARs]
regions.X = X:60001-2699520,X:154931044-155260560
regions.Y = Y:10001-2649520,Y:59034050-59363566
[genomes]
defaultGenome
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
chrAllFile = <>
defaultGeneModel
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.
[PARs]
regions.<>
regions.<> = <comma separated >