Hi, I 'm trying to impute genotype calls using Beagle and reference panel. I have a likelihood file of genotyped markers and a list of ungenotyped markers (as Beagle documentation says "When imputing ungenotyped markers using a reference panel, the markers file should contain only the markers genotyped in the reference panel"). But execution stopped with "NullPointerException" when only ungenotyped markers were provided as input. But its not complaining when both genotyped and ungenotyped markers are present in markers file. Has anybody experienced same before or its problem with only my dataset? Any suggestion to deal with such scenario? Thanks in advance.