Beagle imputation

Question

[mahlet.teka]

Hi, I'm doing imputation using Beagle. I have a reference population which I use for imputing my target population. my reference population is a combination of different populations and so before using it as a reference pop, I had to impute the missing markers.Once the reference population is imputed, I then used it to impute my target pop. But when I try to do that, Beagle is giving me an error message that a sample is duplicated. I checked if there is any duplicated sample in both the reference and target population and there seems to be no duplicates. And I don't receive this error message when I impute the target population without the reference population or when I impute the reference population itself. Any idea why this is happening?

Answer 1

[b.contreras.moreira]

Is your input a single merged VCF file? If so you can use the following to check for repeated sample names:

bcftools query -l input.vcf | sort | uniq -c

[mahlet.teka]

b.contreras.moreira, thank you for your response. I did run the above code and found out that there are no duplicates. Its just weird :(