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, 17:16, 15 November 2016
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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 |
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| 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. |
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− | 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/". |
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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. | + | 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 |
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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". |