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ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].
ownload the reference files from this link [http://csg.sph.umich.edu/GREGOR/ GREGOR Download].
Reference files is created by populations(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).
Reference files are created for the different population groups(AFR, AMR, ASN, EUR, SAN) from 1000G data (Release date : May 21, 2011).
If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.
If your LD r2 threshold equals or greater than 0.7, please download reference files from category: LD window size = 1MB; LD r2 ≥ 0.7.
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
BATCHTYPE = slurm
POPULATION = AFR ## define the population, you can specify EUR, AFR, AMR or ASN
BATCHOPTS = --partition=main --time=0:30:0
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
In the config file, there are several parameters to adjust:
In the config file, there are several parameters to adjust:
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 ≥ 0.7， you can define this number between 1 and 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".
BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.
BEDFILE_IS_SORTED: True or false, depending on whether the BED files listed in the index file are sorted.
POPULATION: If you use reference file "AFR", define this to AFR. You have 5 optiones: AFR, AMR, ASN, EUR and SAN.
GREGOR can run on local machine or on the cluster with MOSIX or SLURM.
BATCHTYPE: When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".
BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"
BATCHOPTS: This parameter works with BATCHTYPE when you specify "mosix" or "slurm". For example, when you define mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"
