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* Now, we are ready for meta-analysis. To perform single variant and gene-level meta-analyses all at once, use the following command:
* Now, we are ready for meta-analysis. To perform single variant and gene-level meta-analyses all at once, use the following command:
raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT
raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file \
--SKAT --burden --MB --VT --longOutput --tabulateHits --hitsCutoff 1e-05 \
--prefix COMBINED.QT1 --hwe 1.0e-05 --callRate 0.95 -
This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some PDF files summarizing results.
This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some PDF files summarizing results.
