I'm wondering if imputation, specifically Beagle, needs a reference panel that matches the sample's ancestry group. For example, Beagle documentation suggests the 1000 Genomes Project phase 3 reference panel, which contains all ancestry groups. Is this acceptable to use to impute the genome of, say, an East Asian, African, and European?


2 Answers 2


Basically, yes, you will get better results if you use a reference panel which contains samples with similar ancestry to your targets.

We demonstrated that using TOPMed sequencing data as the imputation reference panel improves genotype imputation quality in these populations[Hispanic/Latino and African], which subsequently enhanced gene-mapping power for complex traits. For rare variants with minor allele frequency (MAF) < 0.5%, we observed a 2.3- to 6.1-fold increase in the number of well-imputed variants, with 11-34% improvement in average imputation quality, compared to the state-of-the-art 1000 Genomes Project Phase 3 and Haplotype Reference Consortium reference panels.

From this paper.


in my experience you should use a publicly cited reference genome like GRCh37 or GRCh38



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  • 1
    $\begingroup$ I use GRCh37 but I need to use a reference panel in addition to a reference genome $\endgroup$
    – BigMistake
    May 23 at 20:32
  • $\begingroup$ The question asks about a reference panel, not a reference genome. $\endgroup$
    – user438383
    May 24 at 8:49

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