Changes

   ## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY

   ## KEY ELEMENTS TO CONFIGURE : NEED TO MODIFY

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   INDEX_SNP_FILE = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.index.snps.rsid.list.txt    ## e.g. /home/myid/data/FallInBed/example.snp.txt

   INDEX_SNP_FILE = /workingdirectory/example/example.index.snps.rsid.list.txt    ## e.g. /workingdirectory/example/example.index.snps.rsid.list.txt

   BED_FILE_INDEX = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/example/example.bed.file.index ## e.g. /home/myid/data/FallInBed/bedfiles.index

   BED_FILE_INDEX = /workingdirectory/example/example.bed.file.index ## e.g. /workingdirectory/example/example.bed.file.index

   REF_DIR = /net/dumbo/home/jchen/prj/chiseq/codes/FallInBed_Binomial/ref/ ## reference directory

   REF_DIR = /workingdirectory/ref/ ## reference directory

   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 = /workingdirectory/example/example.rsid.20130808/ ## e.g. /workingdirectory/example/example.rsid.20130808/

   MIN_NEIGHBOR_NUM = 500

   MIN_NEIGHBOR_NUM = 500

   BEDFILE_IS_SORTED = True

   BEDFILE_IS_SORTED = True

REF_DIR: Define reference file directory which you download at here.

REF_DIR: Define reference file directory which you download at here.

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 (and control 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".  

MIN_NEIGHBOR_NUM: Define neighbor number around index SNP. Script will find no less than this number around every index SNP.

MIN_NEIGHBOR_NUM: Define the minimum number of control SNPs for each index SNP. Script will find no less than this number around every index SNP.  If you make this number of control SNPs very large, the control SNPs will be less closely matched on the three matching properties (distance to nearest gene, frequency and number of SNPs in LD).

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.