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mLine 70:
Line 70: − RANDOM_LIST_NUM = 1000 Line 76:
Line 75: − + − Line 84:
Line 82: − − RANDOM_LIST_NUM: Define how many random lists, e.g. 100 or 1000
no edit summary
R2THRESHOLD = 0.7
R2THRESHOLD = 0.7
LDWINDOWSIZE = 1000000
LDWINDOWSIZE = 1000000
OUT_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.rsid.20130808/ ## e.g. /home/myid/data/FallInBed/result/
OUT_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.rsid.20130808/ ## e.g. /home/myid/data/FallInBed/result/
MIN_NEIGHBOR_NUM = 500
MIN_NEIGHBOR_NUM = 500
MOSRUN = mosbatch -E/tmp -i -m2000 -j20,43,122,135,137,138,149,151,153,154,155,156,162,163 sh -c
MOSRUN = mosbatch -E/tmp -i -m2000 -j20,43,122,135,137,138,149,151,153,154,155,156,162,163 sh -c
In the config file, there are several parameters to adjust:
In the configure file, there are 8 parameters to adjust:
INDEX_SNP_FILE: This file lists the trait-associated input SNPs. In this file, there is a single column without a header. Index SNPs can be in rsid or chr:pos format.
INDEX_SNP_FILE: This file lists the trait-associated input SNPs. In this file, there is a single column without a header. Index SNPs can be in rsid or chr:pos format.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.
R2THRESHOLD and LDWINDOWSIZE: These two parameters define the index SNP LD proxies by R2 threshold and LD window size.
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".
