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?
$\begingroup$
$\endgroup$
Add a comment
|
2 Answers
$\begingroup$
$\endgroup$
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.
$\begingroup$
$\endgroup$
2
in my experience you should use a publicly cited reference genome like GRCh37 or GRCh38
https://www.sciencedirect.com/science/article/pii/S0888754317300058
New contributor
zhiguang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
-
1$\begingroup$ I use GRCh37 but I need to use a reference panel in addition to a reference genome $\endgroup$ May 23 at 20:32
-
$\begingroup$ The question asks about a reference panel, not a reference genome. $\endgroup$ May 24 at 8:49