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, 12:40, 15 August 2013
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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 |
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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 --studyName your.studyName.file --writeVcf --prefix yourPrefix |