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raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT
raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT
--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits
--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1
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 annotated PDF files summarizing results (--labelHits).
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.
* The following output will be generated:
* The following output will be generated:
