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gpf_instance.yaml
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vars:
instance_id: data_hg38_public
instance_id: '%(instance_id)s'
genotype_storage:
default: duckdb_sd
storages:
- id: duckdb_sd
storage_type: duckdb2
db: sequencing_de_novo.duckdb
read_only: true
base_dir: '%(wd)s/duckdb_storage'
- id: duckdb_parquet
storage_type: duckdb2
annotation:
conf_file: '%($DAE_DB_DIR)s/annotation.yaml'
studies:
dir: '%($DAE_DB_DIR)s/studies'
datasets:
dir: '%($DAE_DB_DIR)s/datasets'
default_study_config:
conf_file: '%($DAE_DB_DIR)s/defaultConfiguration.yaml'
gene_profiles_config:
conf_file: '%($DAE_DB_DIR)s/geneProfiles.yaml'
reference_genome:
resource_id: hg38/genomes/GRCh38-hg38
gene_models:
resource_id: hg38/gene_models/refGene_v20170601
gene_sets_db:
gene_set_collections:
- gene_properties/gene_sets/autism
- gene_properties/gene_sets/relevant
- gene_properties/gene_sets/sfari
- gene_properties/gene_sets/spark
- gene_properties/gene_sets/MSigDB_curated
- gene_properties/gene_sets/miRNA
- gene_properties/gene_sets/GO
- gene_properties/gene_sets/domain
- gene_properties/gene_sets/disease
- gene_properties/gene_sets/miRNA_Darnell
gene_scores_db:
gene_scores:
- gene_properties/gene_scores/LGD
- gene_properties/gene_scores/RVIS
- gene_properties/gene_scores/pLI
- gene_properties/gene_scores/pRec
- gene_properties/gene_scores/SFARI_gene_score
- gene_properties/gene_scores/Satterstrom_Buxbaum_Cell_2020
- gene_properties/gene_scores/Iossifov_Wigler_PNAS_2015
gene_profiles_config:
conf_file: '%($DAE_DB_DIR)s/geneProfiles.yaml'
gpfjs:
visible_datasets:
- ALL_genotypes
- sequencing_de_novo
- SD_autism
- SD_autism_ssc
- SD_autism_spark
- SD_autism_other
- SD_congenital_heart_disease
- SD_developmental_disorder
- SD_epilepsy
- SD_intellectual_disability
- SD_schizophrenia
- SD_ACS2014_liftover
- SD_AGRE_WG38_859_DENOVO
- SD_Chung2015CHD_liftover
- SD_DDD2017_liftover
- SD_EichlerTG2012_liftover
- SD_EichlerWE2012_liftover
- SD_Epi4KWE2013_liftover
- SD_GulsunerSchWE2013_liftover
- SD_IossifovWE2014_liftover
- SD_KarayiorgouWE2012_liftover
- SD_Krumm2015_SNVindel_liftover
- SD_Lelieveld2016_liftover
- SD_ODonovanWE2014_liftover
- SD_ORoakTG2014_SSC_liftover
- SD_ORoakTG2014_TASC_liftover
- SD_SFARI_SSC_WGS_CSHL_DENOVO
- SD_VissersWE2012_liftover
- SD_Yuen2017_liftover
- SD_iWES_v1_1_genotypes_DENOVO
- SD_Helbig2016_liftover
- SD_McCarthy2014_liftover
- SD_Rauch2012_liftover
- SD_Takata2018_liftover
- SD_Turner2017_liftover
- SD_Werling2018_liftover