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Reference panelLatest30 May 2025Mamana Mbiyavanga

H3Africa v7

H3Africa v7 reference panel. 4,283 samples, 69.6M variants, hg38. The most recent H3Africa panel, adding the TrypanoGEN, CAfGEN and MalariaGEN cohorts to the v6 sources (KGP, HGDP, 54gene, GAPW, SAALS, AWI-Gen, H3A).

4,283
Samples
69.6M
Variants
hg38
Build

Reference panel information

Chromosomes
1-22
Biallelic SNPs
69,576,934
Samples
4,283
Haplotypes
8,566

Sample size by population

African regions

  • East Africa (158)
  • West Africa (1078)
  • North Africa (40)
  • Central Africa (80)
  • Southern Africa (314)

Europe

  • European (551)

Asia

  • East Asian (747)
  • South Asian (630)

Americas

  • Admixed American (654)

Oceania

  • Oceanian (25)
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Variant distribution

Input variant composition

SNPs
159.2M
Other
2.4M
Indels
19.1M
Multiallelic
14.8M

Variants per chromosome

1
5.8M
2
5.8M
3
4.7M
4
4.6M
5
4.3M
6
4.0M
7
4.1M
8
3.7M
9
3.3M
10
3.5M
11
3.6M
12
3.3M
13
2.5M
14
2.1M
15
2.1M
16
2.3M
17
2.3M
18
2.2M
19
1.5M
20
1.7M
21
1.0M
22
1.1M

QC filtering funnel

Input
175.7M
SNP filter
148.7M
Missingness filter
144.3M
Min-AC filter
71.2M
Final (phased)
69.6M

Populations

Global (6 continents, 5 African regions, 39% African).

How it works

  1. Sign in (or register) for a FedImpute account.
  2. Prepare your GWAS genotypes as VCF on the GRCh38 (hg38) build (or lift over at submission).
  3. Start a New Imputation Job and select this panel.
  4. FedImpute phases your genotypes (Eagle) and imputes against the panel (Minimac4).
  5. Download your phased and imputed genotypes as VCF.

Explore more

Reference panel

Reference Panels on FedImpute

A high-level guide to the reference panels available on FedImpute, highlighting the latest H3Africa v7 panel.

Reference panel

H3Africa v6 African-only

African-only subset of H3Africa v6. 1,895 samples from 48 African populations, 42.3M variants, hg38. Includes 54gene, GAPW, SAALS, AWI-Gen, H3A consortium cohorts.

Reference panel

H3Africa v6 (full)

Full H3Africa v6 reference panel. 4,447 samples across African and global populations, 58.7M variants, hg38. Includes KGP, HGDP, 54gene, GAPW, SAALS, AWI-Gen cohorts.

Reference panel

1KG NYGC 30x

1000 Genomes Project, NYGC 30x high-coverage re-sequencing. 3,202 samples, 31.3M variants, hg38. Good for non-African ancestry imputation. ALL-population allele frequencies only in this release; per-superpopulation breakdown coming later.