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The documentation for VariantsToBinaryPed states, in the section about the --metaData command:
Regardless of which file is specified, the walker will output a .fam file alongside the bed file. If the command line has "-md [name].fam", the fam file will be subset and reordered to match the sample content and ordering of the VCF. However, if a metadata file of the alternate format is passed by "-md [name].txt", the walker will construct a formatted .fam file from the data.
There is no option called
-md, right? I think this should be about the