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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.
==== Association Methods====
==== Association Options====
* 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.
* 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.
==== Conditional Analysis====
==== Conditional Analysis====
* To decide whether a signal is caused by shadowing a significant common variant nearby, '''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.
* To decide whether a signal is caused by shadowing a significant common variant nearby, '''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.
