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The headers are not keywords and will be omitted by the program. You can use one of the --extract options ( Data management ) to limit the COJO analysis in a certain genomic region. The output format is the same as that from --cojo-slct.
This option is only valid in conjunction with the option --cojo-slct. It is assumed that SNPs more than d Kb away from each other are in complete linkage equilibrium.