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config.yml
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---
############################################################################################################################
#################################################### INFORMATION ###########################################################
############################################################################################################################
# All file paths accept absolute and relative paths, although absolute paths are preferred.
# Environment variables (including ~) are not processed.
############################################################################################################################
############################################ RUN COMMON VARIABLES ##########################################################
############################################################################################################################
# Folder where all the outputs are saved (COLOC, MR results files, etc.)
# csMR will write the analysis results into <BASE_OUTPUT_DIR>/precomputation, <BASE_OUTPUT_DIR>/COLOC and <BASE_OUTPUT_DIR>/MR subdirectories respectively. The directory and its subdirectories will be created if they do not exist.
BASE_OUTPUT_DIR: csMR-EXAMPLE
### eQTL_INPUT: list of eQTL files
# id: identifier for the dataset. *MUST be unique and NO double dash allowed.
# path: filepath to the QTL data. *Compressed files are not allowed.
eQTL_INPUT: # eQTL summary file must contain "SNP, A1, A2, MAF, BETA, SE, P, N, GENE" columns.
- id: Astrocyte
path: example/single-cell-eQTL/sceQTL_brain_Astrocyte.chr1.ma
- id: ExN
path: example/single-cell-eQTL/sceQTL_brain_Excitatory.neurons.chr1.ma
### GWAS_SUMSTATS:
# id: identifier for GWAS. *MUST be unique and NO double dash allowed.
# path: filepath to GWAS sumstats. *Compressed files are not allowed.
GWAS_SUMSTATS: # GWAS summary file must contain "SNP, A1, A2, MAF, BETA, SE, P, N" columns.
- id: BMI_Giant_UKB
path: example/BMI_GWAS/BMI_giant_ukbb_combined_2018.chr1.ma
type: quant
OUTCOME_DIR: ### path to outcome summary stats. The required file format is the same as GWAS summary file.
example/outcomes
GWAS_REFERENCE_GENOTYPE: # specify path to reference genotype and provide duplicated snp files if available.
path:
data/reference_genome_1000G_EUR
duplicated_snp_path: #if not applicable type "None".
None
eQTL_REFERENCE_GENOTYPE:
data/reference_genome_1000G_EUR
# Parameters for colocalization analysis
COLOC_SETTING: # Window definition for mapping gene specificity values to SNPs
WINDOW_SIZE_BP:
100000
COVERAGES: # Multiple coverages are allowed which must be separated by comma. eg: 0.6,0.9
0.9
THREADS:
5
CUTOFF:
0.8