Changes

=====List of Studies=====

=====List of Studies=====

* --studyName option is crucial for '''RAREMETAL''' to work. Ignoring this option would lead to FATAL ERROR and '''RAREMETAL''' would stop.  

* --summaryFiles option is crucial for '''RAREMETAL''' to work. Ignoring this option would lead to FATAL ERROR and '''RAREMETAL''' would stop.  

* The file should contain the path and prefix of the studies you want to include.  

* The file should contain the path and prefix of the studies you want to include.  

* If there is one or more studies that you want to excluded from your list, but want to save some effort of generating a new file, you can put a "#" in front of the line of record. '''RAREMETAL''' would automatically exclude that study from meta analysis.

* If there is one or more studies that you want to excluded from your list, but want to save some effort of generating a new file, you can put a "#" in front of the line of record. '''RAREMETAL''' would automatically exclude that study from meta analysis. An example list of summary file is in the following:

* An example file is in the following:

   /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG

   /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.score.txt.gz

   #/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/HUNT/RareMetalWorker/HUNT_MI_case.TG

   #/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/HUNT/RareMetalWorker/HUNT_MI_case.TG.singlevar.score.txt.gz

* The above example study name file guides '''RAREMETAL''' to look for summary statistics from TwinsUK study only, because "HUNT" study is commented out. The following two files are needed for '''RAREMETAL''' to perform further analysis together with their tabix index file are needed.

* When gene-level analysis is requested, --covFiles option should be used to specify the covariance files. An example file is:

   /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.cov.txt.gz

   /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.cov.txt.gz

   /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.score.txt.gz.tbi

   #/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/HUNT/RareMetalWorker/HUNT_MI_case.TG.singlevar.cov.txt.gz

  /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.cov.txt.gz.tbi

 

* The above example study name file guides '''RAREMETAL''' to look for summary statistics from TwinsUK study only, because "HUNT" study is commented out. The following two files are needed for '''RAREMETAL''' to perform further analysis together with their tabix index file are needed.

=====Group Rare Variants=====

=====Group Rare Variants=====