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Possible bug in BeagleOutputToVCF
It appears that BeagleOutputToVCF does not produce the expected result for the very first variant. Looking a little into it, I found out that the problem stems form the beagle.r2 file not having a header and the first line been treated as such instead of being read as a variant. Adding a bogus header line in the beagle.r2 file seems to be a fine workaround.