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* To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized.
* To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized.
==== Methods ====
==== Methods Options====
* Currently, four methods are provided in '''rareMETAL''', CMC type burden test, Madsen-Browning burden test, Variable Threshold burden test, and SKAT.
* Currently, CMC type burden test, Madsen-Browning burden test, Variable Threshold burden test and SKAT are provided in '''rareMETAL''', by specifying --burden, --MB, --VT and --SKAT.
* '''rareMETAL''' also enables conditional analysis with a list of variants to be conditioned upon provided in a file as input for --condition option. An example input file should be space or tab delimited as in the following. When alleles do not match the ref and alt alleles from samples, the variant will be skipped from conditional analysis.
1:861349:C:T 1:905901:G:A 20:986998:G:C 22:3670691:A:G
== Additional Analysis Options ==
== Additional Analysis Options ==
