2,004
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→STEP 3: Run RAREMETAL for Meta-Analysis
myresult/tutorial.example.QT1.meta.tophits.MB.tbl
myresult/tutorial.example.QT1.meta.tophits.MB.tbl
myresult/tutorial.example.QT1.raremetal.log
myresult/tutorial.example.QT1.raremetal.log
* To do conditional analysis, we just have to add --condition conditionfile, where conditionfile contains the variant that we want to condition upon in the following format:
9:505484545:C:T
Then extra columns of conditional analysis results will be saved in the output file "myresult/tutorial.example.QT1.meta.singlevar.results".
* Please refer to the RAREMETAL [[RAREMETAL_Documentation#Gene-level_Tests_Meta-Analysis_Output|'''documentation''']] for detailed description of output format.
* 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 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 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.
* 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.
