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config.R
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config.R
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#####################
# configuration file
#####################
# process paramerters
mem=64000
threads=16
#####################
# FILE PATHS
### R library files ###
R_LIB = "~/R/x86_64-pc-linux-gnu-library/4.0/"
### General ###
QC_DIR="~/QC" # quality controlled pgen sample and variant files
PHENO_DIR="~/Phenotypes" # phenotype files
GWAS_DIR="~/GWAS_Results" # summary statistics, results, intermediate tables
# mash and PGS files directories are subdirectories of $GWAS_DIR/{phenotype}/
### ENSEMBL annotation files ###
ENSEMBL="~/ensembl-vep" # ensembl vep github (https://github.com/Ensembl/ensembl-vep.git)
ENSEMBL_CACHE="~/cache" # homo_sapiens_CRCh37.vcf cache
### LDSC files ###
LDSC_DIR="~/ldsc" # ldsc github (https://github.com/bulik/ldsc.git)
LDSC_FILE="~/LD_files" # results from LDSC regression
LD_SCORE="~/LD_scores" # LD scores
LD_1000G="~/1000G/all_phase3" # 1000 genomes phase 3 bfile (all_phase3 is a prefix for the bfiles, not folder)
### SELECTION ###
SEL_DIR="~/selection" # sexually-antagonistic selection results
### SIMULATION COVARIANCE ###
SIM_COV="~/sim_cov" # simulation covariance results