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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]. |
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− | 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). |
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| 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. |
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| ############################################################################### | | ############################################################################### |
| BATCHTYPE = local ## run jobs on local machine | | BATCHTYPE = local ## run jobs on local machine |
− | BATCHTYPE = slurm
| + | |
− | BATCHOPTS = --partition=main --time=0:30:0
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| In the config file, there are several parameters to adjust: | | In the config file, there are several parameters to adjust: |
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| 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/". | | 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/". |
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− | 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 | + | 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. |
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| 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". |
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| 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. |
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− | BATCHTYPE: We have three options for this parameter. When you run GREGOR on local machine, specify "local"; when run on MOSIX system, specify "mosix"; when run on SLURM system, specify "slurm".
| + | POPULATION: If you use reference file "AFR", define this to AFR. You have 5 optiones: AFR, AMR, ASN, EUR and SAN. |
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| + | 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". |
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| 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" |