Changes

                                 --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2

                                 --traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2

==STEP 3: Run RAREMETAL to do Meta-Analysis==

==STEP 3: Run RAREMETAL for Meta-Analysis==

* In this step, we run RAREMETAL to meta-analyze two studies without using any of raw data.

* In this step, we run RAREMETAL to meta-analyze two studies without using any of raw data.

* First, we perform single variant and four type of gene-level meta-analysis all at once, using the following command line:

* First, we perform single variant and four type of gene-level meta-analysis all at once, using the following command line:

   cd raremetal

   cd raremetal

   $yourRAREMTALpath/bin/raremetal --studyName studyname.list --groupFile group.file --SKAT --burden --MB --VT  

   $yourRAREMTALpath/bin/raremetal --studyName studyname.list --groupFile group.file --SKAT --burden --MB --VT  

                                   --longOutput --tabulateHits --hitsCutoff 1e-05 --hwe 1.0e-05 --callRate 0.95 --prefix yourprefix.QT1

                                   --hwe 1.0e-05 --callRate 0.95 (# QC options)

                                  --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix yourprefix.QT1 (#output options)

                                  --mapFile ../refFlat_hg19.txt.gz

* First, modify the example.studyname file to make the output files of RareMetaWorker reachable by RareMETAL.

 

* If gene-level meta analysis is expected, then annotation information or groups of variants are necessary. RareMETAL can take group file to get this piece of information. * An example group file is in the following:

  $yourLocaPath/raremetal_tutorial/inputfiles/nonsyn.stop.splice.groupfile

 

* RareMETAL allows filtering single variants to be included in meta analysis according to their QC information summarized by raremetalworker, including HWE p-value and genotype call rate.  

* Finally, to meta-analyze the above two samples using summary statistics, the following command will generate results from single variant meta analysis, gene-level meta analysis using SKAT, Madsen-Browning burden test, simple burden test, Variable Threshold Burden tests.

* The following output are generated

   $yourPath/bin/raremetal --studyName --$yourLocaPath/raremetal_tutorial/inputfiles/example.studyname

  yourprefix.meta.plots.pdf (## QQ plots and manhattan plots from both single variant and gene-level meta-analysis)

    --groupFile $yourLocaPath/raremetal_tutorial/inputfiles/nonsyn.stop.splice.groupfile --SKAT --VT --burden --MB --maf 0.05 --hwe 1.0e-05 --callRate 0.95

  yourprefix.meta.singlevar.results

    --prefix $yourLocaPath/raremetal_tutorial/results/

   yourprefix.meta.burden.results

* To generate a lengthy results and report hits, the following command should be used:

  yourprefix.meta.SKAT.results

   $yourPath/bin/raremetal --studyName --$yourLocaPath/raremetal_tutorial/inputfiles/example.studyname

  yourprefix.meta.VT.results

    --groupFile $yourLocaPath/raremetal_tutorial/inputfiles/nonsyn.stop.splice.groupfile --SKAT --VT --burden --MB --maf 0.05 --hwe 1.0e-05 --callRate 0.95

  yourprefix.meta.MB.results

    --longOutput --tabulateHits --hitsCutoff 1.0e-05 --prefix $yourLocaPath/raremetal_tutorial/results/

   yourprefix.meta.tophits.SKAT.tbl

* Please refer to the documentation for detailed description of output format. [http://genome.sph.umich.edu/wiki/Rare-Metal#Output_Files '''RareMETAL Results''']

  yourprefix.meta.tophits.VT.tbl

  yourprefix.meta.tophits.burden.tbl

  yourprefix.meta.tophits.MB.tbl

  yourprefix.raremetal.log

* Please refer to the RAREMETAL [[RAREMETAL_Documentation#Gene-level_Tests_Meta-Analysis_Output|'''documentation''']] for detailed description of output format.  

* RAREMETAL also takes annotated VCF as input to parse variant grouping information. Please refer to software [[RAREMETAL_Documentation#Group_Rare_Variants_from_Annotated_VCF|'''documentation''']] for details.

* RareMETAL also allows users to output an VCF file of the super set of all variants and use their favorite annotation tool to annotate it and then come back to RareMETAL for the gene-level meta analysis. --writeVCF is the option to use. Please refer to [http://genome.sph.umich.edu/wiki/Rare-Metal#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal '''Write VCF and Annotated outside RareMETAL''']

* RAREMETAL allows users to output an VCF file of the super set of all variants and use their favorite annotation tool to annotate it and then come back to RAREMETAL for the gene-level meta analysis. [[RAREMETAL_Documentation#Generate_a_VCF_File_to_Annotate_Outside_of_Rare_Metal|'''--writeVCF''']] is the option to use.