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→STEP 3: Run RareMETAL to do Meta Analysis
* RareMETAL also takes annotated VCF as input to parse variant grouping information. Please refer to software documentation for details [http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File '''grouping from annotated VCF''']
* RareMETAL also takes annotated VCF as input to parse variant grouping information. Please refer to software documentation for details [http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File '''grouping from annotated VCF''']
* 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.
$yourPath/bin/raremetal --studyName --$yourLocaPath/raremetal_tutorial/inputfiles/example.studyname
--groupFile $yourLocaPath/raremetal_tutorial/inputfiles/nonsyn.stop.splice.groupfile --SKAT --VT --burden --MB --maf 0.05 --hwe 1.0e-05 --callRate 0.95
--prefix $yourLocaPath/raremetal_tutorial/results/
* To generate a lengthy results and report hits, the following command should be used:
$yourPath/bin/raremetal --studyName --$yourLocaPath/raremetal_tutorial/inputfiles/example.studyname
--groupFile $yourLocaPath/raremetal_tutorial/inputfiles/nonsyn.stop.splice.groupfile --SKAT --VT --burden --MB --maf 0.05 --hwe 1.0e-05 --callRate 0.95
--longOutput --tabulateHits --hitsCutoff 1.0e-05 --prefix $yourLocaPath/raremetal_tutorial/results/
* Please refer to the documentation for detailed description of output format. [http://genome.sph.umich.edu/wiki/Rare-Metal#Output_Files '''RareMETAL Results''']
