logLevel: "INFO"
logFile: null
## number of seconds that session remains open
sessionDuration: 1200
## Default study when -s, --study are empty, e.g. "reference_grch37:1kG_phase3"
defaultStudy: ""
## Alias to different studies, these can be fully qualified: user@project:study
alias:
1kg_grch37: hgvauser@reference_grch37:1kG_phase3
1kg_grch38: reference_grch38:1kG_phase3
## The default organism values can be defined here.
organism:
taxonomyCode: ${OPENCGA.CLIENT.ORGANISM.TAXONOMY_CODE}
scientificName: ${OPENCGA.CLIENT.ORGANISM.SCIENTIFIC_NAME}
commonName: ${OPENCGA.CLIENT.ORGANISM.COMMON_NAME}
assembly: ${OPENCGA.CLIENT.ORGANISM.ASSEMBLY}
## REST client configuration options
rest:
host: "${OPENCGA.CLIENT.REST.HOST}"
batchQuerySize: 200
timeout: ${OPENCGA.CLIENT.REST.TIMEOUT}
defaultLimit: 2000
## gRPC configuration options
grpc:
host: "${OPENCGA.CLIENT.GRPC.HOST}"
## Configure the default behaviour when query variants
variant:
unknownGenotype: "0/0"
# each study can have a different format
includeFormats:
1kg_grch37: "GT,AD,DP,GQ"