Hi, I was trying o impute an inbred population with a reference panel using Beagle5.2, both files are .vcf format, the command that I run is:

java -Xss1g -Xmx50g -jar programas/beagle.28Jun21.220.jar err=0.1 iterations=10 ref=ref.vcf gt=population.vcf out=population_imputed

I get an error: unphased or missing genotype for reference sample Arcadia.s.bam at marker [chr1H 89912 . A T]

There is no missing data on the reference panel, does anyone know how I can solve the phase problem.