Changes

   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: [[https://statgen.sph.umich.edu/wiki/Raremetal#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: [[http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File 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

== Q & A ==

== Q & A ==