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./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 --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
* 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 '''Rare Metal''' 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 --studyName your.studyName.file --writeVcf --prefix yourPrefix
