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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 --studyName your.studyName.file --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#Grouping_from_an_Annotated_VCF_File|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 --studyName your.studyName.file --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing/stop --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix
