Step 2: performing genome-wide set-based association tests. Multiple genes are tested simultaneously for computation speed-up

• Same as the genome-wide single-variant tests, –GMMATmodel_varianceRatio_multiTraits_File can be used
• Additional input –groupFile= is needed with the following parameters to run set-based tests:

	--maxMAF_in_groupTest=0.1   \
        --minMAF_in_groupTest_Exclude=0       \
        --groupFile=${groupFile}        \
        --annotation_in_groupTest=null  \
        --MACCutoff_to_CollapseUltraRare=10     \
        --is_single_in_groupTest=TRUE  \
        --is_equal_weight_in_groupTest=TRUE    \
        --LOCO=FALSE    \

Output files

The program will generate one output file for each of the tested genes.