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Jump to navigationJump to search→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.
* Before doing analysis, open raremeta/studyname.list and modify the prefix with the right path. The file should look like
* Prepare the raremetalworker results for meta-analysis using the following command:
bgzip yourprefix.example1.QT1.singlevar.score.txt
bgzip yourprefix.example1.QT1.singlevar.score.txt
tabix -c "#" -s 1 -b 2 -e 2 yourprefix.example1.QT1.singlevar.score.txt.gz
tabix -c "#" -s 1 -b 2 -e 2 yourprefix.example1.QT1.singlevar.score.txt.gz
bgzip yourprefix.example1.QT1.singlevar.cov.txt
bgzip yourprefix.example1.QT1.singlevar.cov.txt
tabix -c "#" -s 1 -b 2 -e 2 yourprefix.example1.QT1.singlevar.cov.txt.gz
tabix -c "#" -s 1 -b 2 -e 2 yourprefix.example1.QT1.singlevar.cov.txt.gz
* Before doing analysis, open raremetal/summaryfiles and modify the prefix with the right path. The file should look like
$yourpath/raremetal_tutorial/raremetalworker/output/example1.QT1.singlevar.score.txt.gz
$yourpath/raremetal_tutorial/raremetalworker/output/example1.QT2.singlevar.score.txt.gz
* Then open raremetal/covfiles and modify the prefix with the right path. The file should look like
$yourpath/raremetal_tutorial/raremetalworker/output/example1.QT1.singlevar.cov.txt.gz
$yourpath/raremetal_tutorial/raremetalworker/output/example1.QT2.singlevar.cov.txt.gz
* Now, we are ready for meta-analysis. To perform single variant and four type of gene-level meta-analysis all at once, use the following command line:
* Now, we are ready for meta-analysis. To perform single variant and four type of gene-level meta-analysis all at once, use the following command line:
cd raremetal
cd raremetal
$yourRAREMTALpath/bin/raremetal --studyName studyname.list --groupFile group.file --SKAT --burden --MB --VT
$yourRAREMTALpath/bin/raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT
--hwe 1.0e-05 --callRate 0.95 (# QC options)
--hwe 1.0e-05 --callRate 0.95 (# QC options)
--longOutput --tabulateHits --hitsCutoff 1e-05 --prefix yourprefix.QT1 (#output options)
--longOutput --tabulateHits --hitsCutoff 1e-05 --prefix myresult/tutorial.example.QT1 (#output options)
--labelHits
--labelHits
* The following output are generated
* The following output are generated
myresult/tutorial.example.QT1.meta.plots.pdf (## QQ plots and manhattan plots from both single variant and gene-level meta-analysis with hits labeled)
myresult/tutorial.example.QT1.meta.singlevar.results
myresult/tutorial.example.QT1.meta.burden.results
myresult/tutorial.example.QT1.meta.SKAT.results
myresult/tutorial.example.QT1.meta.VT.results
myresult/tutorial.example.QT1.meta.MB.results
myresult/tutorial.example.QT1.meta.tophits.SKAT.tbl
myresult/tutorial.example.QT1.meta.tophits.VT.tbl
myresult/tutorial.example.QT1.meta.tophits.burden.tbl
myresult/tutorial.example.QT1.meta.tophits.MB.tbl
myresult/tutorial.example.QT1.raremetal.log
* 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.
