Phase a reference panel

Question

[Bettina]

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.

[lieven.sterck]

Hello Bettina,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!