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** callrate.cutoff specifies the call rate cutoffs that will be used. All sites with call rates lower than the cutoff will be labelled as missing.
** callrate.cutoff specifies the call rate cutoffs that will be used. All sites with call rates lower than the cutoff will be labelled as missing.
** hwe.cutoff specifies the cutoffs for call rate, All sites with call rate lower than the cutoff will be labeled as missing.
** hwe.cutoff specifies the cutoffs for call rate, All sites with call rate lower than the cutoff will be labeled as missing.
* Output is a dataframe that consist of the following fields:
** pos: Variant physical position
** ref: Reference allele
** alt: Alternative allele
** no.sample: Number of samples
** p.value: P-values
** statistic: Test statistic (score statistic)
** maf: Minor allele frequency
** beta1.est: Beta estimates
** beta1.sd: The standard deviation for beta estimates
** hsq.est: Locus genetic variance estimates
** direction.by.study: Direction of genetic effects by study
** anno: Annotation for variants
== Performing gene level association test ==
== Performing gene level association test ==
