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If the reference sample is independent from the GWAS samples, it is not valid to approximate the chance correlations between SNPs in the GWAS data by those estimated from the reference sample. 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.