Changes

* 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  

* 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.)

* 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

* 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

* 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

* 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

==Other Useful Info==

==Other Useful Info==