Running Beagle on a VCF with 1 sample
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2.2 years ago
phosphorus ▴ 20

Hello,

I am a new user of Beagle and I am trying to use it on a VCF with 1 patient sample. The VCF contains chromosomes 1-22, X and Y. It contains genotype information for all variants, but phasing information is only available for some variants. I wish to impute the phasing information using Beagle.

When I tried running it through Beagle, the following error message showed:

ERROR: there is only one sample

How can I circumvent this error? Can I subset the VCF by chromosome and merge them so that there are many different samples in the same VCF?

imputation genome beagle • 1.4k views
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phosphorus Wishing You a Happy New Year! Have you managed to address this issue? I'm encountering challenges with phasing a single-sample VCF as well."

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2.2 years ago
4galaxy77 2.8k

You cannot impute variants with a single sample and no reference panel. You need to download a reference panel like the 1000 genomes and use that. Alternatively, use an imputation server like the Michigan Imputation Server or Sanger Imputation Server.

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Thanks a lot! Do you mean that I can impute variants with a single sample as long as I use a reference panel in the 'ref=' flag? I wanted to use the Michigan Imputation Server but it tells me it needs at least 50 samples.

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You cannot use Michigan Imputation Server. You do need a reference panel.

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