About PairWiseLDsetSNP.jar
1. PairWiseLDsetSNP.jar is the java program which calcuates linkage disequilibrium (LD) matrix of spedicifed SNPs from genotype data.


Usage of PairWiseLDsetSNP.jar
1. PairWiseLDsetSNP.jar requires Java environment.
2. Command: "java -jar PairWiseLDsetSNP.jar -file Chr22_Ex -SNPs AssocSNP.txt -Gap 1000000 -Thres 0.5"


Arguments
1. -file : prefix of the genotype file
2. -SNPs : SNP list to be calculated for LD matrix with all the SNPs in the genotype file
3. -Gaps : Maximum position differences of SNP pairs to be calculated for LD (bp).
4. -Thres : Minimum value of r2 to be output in the file. Please set "-Thres -1" if you want to get all LD matrix of the specified SNPs.


The format of input file
1. hoge.geno : A matrix genotype file with PLINK "--recode12 --tab" format, but does not include the initial 6 header columns. (cut -f 7- xx.ped > xx.geno)
2. hoge.info : A SNP position file (any kinds of position information could be included in the second column).
3. AssocSNP.txt : A SNP list for LD calculation. if you want to get all LD matrix, include all the SNPs in xxx.geno/info in this list.


Output files
1. PairWiseLDsetSNP.jar outputs one files.
 (1) hoge_LDdata.txt : This file includes LD matrix of pairwise SNPs.


Any questions to Yukinori Okada (http://plaza.umin.ac.jp/~yokada/datasource/software.htm   yokada@broadinstitute.org)


