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** direction.by.study: Direction of genetic effects by study
** direction.by.study: Direction of genetic effects by study
** anno: Annotation for variants
** anno: Annotation for variants
== Perform single variant association test using a group file ==
Summary level statistics collected in meta-analysis can often be messy, messier for lower frequency variants than for common variants. To correct for the right alleles, and make sure that ref/alt alleles from each study are properly aligned, it is often desirable to
== Performing gene level association test ==
== Performing gene level association test ==
** direction.meta.single.var.out: Direction of meta-analysis statistics for single variant test. It may be useful for inspecting if any of the variant in the gene have opposite effects etc.
** direction.meta.single.var.out: Direction of meta-analysis statistics for single variant test. It may be useful for inspecting if any of the variant in the gene have opposite effects etc.
** pos.ref.alt.out: Position, reference and alternative alleles for each variant position in the gene
** pos.ref.alt.out: Position, reference and alternative alleles for each variant position in the gene
== Perform gene-level test with a group file ==
== Performing conditional analysis for single variant tests ==
== Performing conditional analysis for single variant tests ==
