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Hello, what is the source of your input data?
thank you for your response. I'm using beagle output (.phased files) as input for selscan
Selscan accepts hap, VCF, and TPED formats, so, you need to get your Beagle output into one of those. I'm aware that these types of analyses can be nightmares.
How to convert .phased to .hap file?
Try to understand both formats and then decide what you need to do.