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m2zfast.conf
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# Required programs.
METAL2ZOOM_PATH = "bin/locuszoom.R";
NEWFUGUE_PATH = "new_fugue";
PLINK_PATH = "plink";
RSCRIPT_PATH = "Rscript";
TABIX_PATH = "tabix";
# SQLite database settings.
SQLITE_DB = {
'hg18' : "data/database/locuszoom_hg18.db",
'hg19' : "data/database/locuszoom_hg19.db",
'hg38' : "data/database/locuszoom_hg38.db",
};
# GWAS catalog files
GWAS_CATS = {
'hg18' : {
'whole-cat_significant-only' : {
'file' : "data/gwas_catalog/gwas_catalog_hg18.txt",
'desc' : "The NHGRI GWAS catalog, filtered to SNPs with p-value < 5E-08"
}
},
'hg19' : {
'whole-cat_significant-only' : {
'file' : "data/gwas_catalog/gwas_catalog_hg19.txt",
'desc' : "The EBI GWAS catalog, filtered to SNPs with p-value < 5E-08"
}
},
'hg38' : {
'whole-cat_significant-only' : {
'file' : "data/gwas_catalog/gwas_catalog_hg38.txt",
'desc' : "The EBI GWAS catalog, filtered to SNPs with p-value < 5E-08"
}
},
'hg38_151' : {
'whole-cat_significant-only' : {
'file' : "data/gwas_catalog/gwas_catalog_hg38_151.txt",
'desc' : "The EBI GWAS catalog, filtered to SNPs with p-value < 5E-08"
}
}
}
# Location of genotypes to use for LD calculations.
LD_DB = {
# COVID_rel2
'COVID2_Italy_Norway_Spain' : {
'hg38' : {
'ITALY_NORWAY_SPAIN' : {
'bim_dir' : "/work_ifs/sukmb299/references/locuszoom/data_release2_noMAF/Italy_Norway_Spain/hg38",
}
},
'hg38_151' : {
'ITALY_NORWAY_SPAIN' : {
'bim_dir' : "/work_ifs/sukmb299/references/locuszoom/data_release2_noMAF/Italy_Norway_Spain/hg38",
}
}
},
# 1000G phase 3
'1000G_Nov2014' : {
'hg19' : {
'EUR' : {
'bim_dir' : "data/1000G/genotypes/2014-10-14/EUR/",
},
'ASN' : {
'bim_dir' : "data/1000G/genotypes/2014-10-14/ASN/",
},
'AFR' : {
'bim_dir' : "data/1000G/genotypes/2014-10-14/AFR/",
},
'AMR' : {
'bim_dir' : "data/1000G/genotypes/2014-10-14/AMR/",
}
},
'hg38' : {
'EUR' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/EUR/",
},
'IBS' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/IBS/",
},
'TSI' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/TSI/",
},
'AFR' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/AFR/",
},
'AMR' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/AMR/",
},
'EAS' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/EAS/",
},
'SAS' : {
'bim_dir' : "data/1000G/genotypes/2017-04-10/SAS/",
}
}
},
'1000G_March2012' : {
'hg19' : {
'EUR' : {
'bim_dir' : "data/1000G/genotypes/2012-03/EUR/",
},
'ASN' : {
'bim_dir' : "data/1000G/genotypes/2012-03/ASN/",
},
'AFR' : {
'bim_dir' : "data/1000G/genotypes/2012-03/AFR/",
},
'AMR' : {
'bim_dir' : "data/1000G/genotypes/2012-03/AMR/",
}
}
},
'1000G_June2010' : {
'hg18' : {
'CEU' : {
'ped_dir' : "data/1000G/genotypes/2010-06/CEU/pedFiles/",
'map_dir' : "data/1000G/genotypes/2010-06/CEU/mapFiles/"
},
'JPT+CHB' : {
'ped_dir' : "data/1000G/genotypes/2010-06/JPT+CHB/pedFiles/",
'map_dir' : "data/1000G/genotypes/2010-06/JPT+CHB/mapFiles/"
},
'YRI' : {
'ped_dir' : "data/1000G/genotypes/2010-06/YRI/pedFiles/",
'map_dir' : "data/1000G/genotypes/2010-06/YRI/mapFiles/"
}
}
},
'hapmap' : {
'hg18' : {
'CEU' : {
'ped_dir' : "data/hapmap/genotypes/2008-10_phaseII/CEU/pedFiles/",
'map_dir' : "data/hapmap/genotypes/2008-10_phaseII/CEU/mapFiles/"
},
'JPT+CHB' : {
'ped_dir' : "data/hapmap/genotypes/2008-10_phaseII/JPT+CHB/pedFiles/",
'map_dir' : "data/hapmap/genotypes/2008-10_phaseII/JPT+CHB/mapFiles/"
},
'YRI' : {
'ped_dir' : "data/hapmap/genotypes/2008-10_phaseII/YRI/pedFiles/",
'map_dir' : "data/hapmap/genotypes/2008-10_phaseII/YRI/mapFiles/"
}
}
}
}