Changes

* 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====

* '''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.

  1:861349:C:T 1:905901:G:A 20:986998:G:C 22:3670691:A:G

  1:861349:C:T 1:905901:G:A 20:986998:G:C 22:3670691:A:G