Changes

  --mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.  

  --mafMin [0.00] and --mafMax [0.50] specify the minimum and maximum allele frequency for variants to group.  

  --mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.

  --mac [0.0] specify the minimum rare allele count as one of the filters to rare variants to group.

  --noStop allows the permutation in VT test  --xLabel [X],

  --noStop indicating no stopping rule to be used in VT permutation test.

                              --Xstart [2699520], --Xend [154931044], --dosage,

  --xLabel [X] specifies labels for chromosome X.

                              --founderFreq, --h2Only, --fullResult [ON]

--Xstart [2699520] and --Xend [154931044] are start and end position of non-pseudo-autosomal region.

--founderFreq considers founder allele frequencies in analysis.

--h2Only provides a shortcut of calculating heritability only.

--fullResult [on] provides results in long format in gene-level association testing, including results from single markers included in analysis.

== Example Command Line ==

== Example Command Line ==