From Genome Analysis Wiki
==== QC Options ====
rareMETAL''' allows filtering of variants from individual studies by their HWE pvalue and call rate, which are generated as part of the output from '''rareMetalWorker''' or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''].
* To filter by HWE p-values, --hwe option should be used. The default is 0.0, which means not filtering any of the variants.
* To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized.