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R2THRESHOLD = 0.7
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
LDWINDOWSIZE = 1000000
OUT_DIR = /workingdirectory/example/example.rsid.20130808/ ## e.g. /workingdirectory/example/example.rsid.20130808/
OUT_DIR = /workingdirectory/example/example.rsid.20130808/
MIN_NEIGHBOR_NUM = 500
MIN_NEIGHBOR_NUM = 500
BEDFILE_IS_SORTED = True
BEDFILE_IS_SORTED = True
POPULATION = AFR ## define the population, you can specify EUR, AFR, AMR or ASN
TOPNBEDFILES = 2
JOBNUMBER = 10
###############################################################################
#BATCHTYPE = mosix ## submit jobs on MOSIX
#BATCHOPTS = -E/tmp -i -m2000 -j10,11,12,13,14,15,16,17,18,19,120,122,123,124,125 sh -c
###############################################################################
#BATCHTYPE = slurm ## submit jobs on SLURM
#BATCHOPTS = --partition=main --time=0:30:0
###############################################################################
BATCHTYPE = local ## run jobs on local machine
BATCHTYPE = slurm
BATCHTYPE = slurm
BATCHOPTS = --partition=main --time=0:30:0
BATCHOPTS = --partition=main --time=0:30:0
BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.
BED_FILE_INDEX: This file lists the datasets (e.g. BED files) to be used for enrichment analysis. Use complete paths to file locations and make sure positions are in hg19 format.
REF_DIR: Define reference file directory which you download at here.
REF_DIR: Define reference file directory which you download at here. If your "AFR" folder is at "/home/myid/GRGORE/ref/AFR/", then define this parameter to "/home/myid/GRGORE/ref/".
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP (and control SNP) LD proxies by r2 threshold and LD window size. If you download r2 &le 0.7
OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
OUT_DIR: All result files are saved to this folder, where the script will create multiple sub-directories. Index SNPs are in the folder "index_SNP"; Random SNPs are in the folder "random_SNP".
