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| * Here is an example command line to do single variant meta analysis only: | | * Here is an example command line to do single variant meta analysis only: |
− | ./raremetal --studyName your.studyName.file --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --prefix yourPrefix |
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| * When you want to do all burden tests using a group file to specify which variants to group: | | * When you want to do all burden tests using a group file to specify which variants to group: |
− | ./raremetal --studyName your.studyName.file --groupFile your.groupfile --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --groupFile your.groupfile --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix |
| (NOTE: this will generate single variant meta analysis result and the short format output for burden test results.) | | (NOTE: this will generate single variant meta analysis result and the short format output for burden test results.) |
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| * Here is how to do all SKAT meta analysis using a group file and request a long format output together with tabulated hits: | | * Here is how to do all SKAT meta analysis using a group file and request a long format output together with tabulated hits: |
− | ./raremetal --studyName your.studyName.file --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --prefix yourPrefix |
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| * Here is an example of adding QC filters to variants when doing meta analysis. | | * Here is an example of adding QC filters to variants when doing meta analysis. |
− | ./raremetal --studyName your.studyName.file --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix |
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| * Here is how to do the same thing but reading grouping information from an annotated VCF file: | | * Here is how to do the same thing but reading grouping information from an annotated VCF file: |
− | ./raremetal --studyName your.studyName.file --annotatedVcf your.annotated.vcf --annotation nonsyn/stop/splicing --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --annotatedVcf your.annotated.vcf --annotation nonsyn/stop/splicing --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix |
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| * If you want to write a VCF file of pooled variants from all studies, annotate them using your favorite annotation program, and then come back to '''RAREMETAL''' with the annotate VCF file to do burden tests: | | * If you want to write a VCF file of pooled variants from all studies, annotate them using your favorite annotation program, and then come back to '''RAREMETAL''' with the annotate VCF file to do burden tests: |
| First, use the following command to write the VCF file: | | First, use the following command to write the VCF file: |
− | ./raremetal --studyName your.studyName.file --writeVcf --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --writeVcf --prefix yourPrefix |
| Second, annotate the VCF file using your favorite annotation program. (Annotated VCF file has to follow the format described here: [[Rare-Metal#Group_Rare_Variants_from_Annotated_VCF|annotated VCF format]]) | | Second, annotate the VCF file using your favorite annotation program. (Annotated VCF file has to follow the format described here: [[Rare-Metal#Group_Rare_Variants_from_Annotated_VCF|annotated VCF format]]) |
| Third, use the following command to do meta analysis: | | Third, use the following command to do meta analysis: |
− | ./raremetal --studyName your.studyName.file --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing/stop --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix | + | ./raremetal --summaryFiles your.list.of.summary.files --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing/stop --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix |
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| ==Other Useful Info== | | ==Other Useful Info== |