About MetaAnalysisGC.jar
1. MetaAnalysisGC.jar is the java program which conducts Genomic Control (GC) corrections to the GWAS result with specified lambda GC value.


Usage of MetaAnalysisGC.jar
1. MetaAnalysisGC.jar requires Java environment.
2. MetaAnalysisGC.jar requires commons-math-1.2.jar. Place it to your external libraly of jre.
3. MetaAnalysisGC.jar requires P_Chi_CorresTable_high.txt at the working directory.
4. Command: "java -jar MetaAnalysisGC.jar -prefix ExampleFile_GC -lambda 1.10"


Arguments
1. -prefix : prefix of the input file
2. -lambda : lambdaGC value to be applied as GC correction


The format of input file
1. A matrix file with one row per SNP with 7 columns
2. Seven columns for SNP association results
  Col 1 : No. cases
  Col 2 : No. controls
  Col 3 : Allele 1 frequency in cases
  Col 4 : Allele 1 frequency in controls
  Col 5 : Beta of Allele 1
  Col 6 : SE for Beta
  Col 7 : P-value
3. For missing value, please input "-99".

Output files
1. MetaAnalysisGC.jar outputs two files.
 (1) hoge_GCed.txt : This file includes GC corrected statistics of the GWAS results.
 (2) hoge_GCed_log.txt : This file includes log information.


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


