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Imputation

Summary Table

NAME CATEGORY CITATION
1000 Genomes Imputation panel 1000 Genomes Project Consortium. "A global reference for human genetic variation." Nature 526.7571 (2015): 68.
HGDP+1kGP Imputation panel Koenig, Z., Yohannes, M. T., Nkambule, L. L., Goodrich, J. K., Kim, H. A., Zhao, X., ... & Martin, A. R. (2023). A harmonized public resource of deeply sequenced diverse human genomes. bioRxiv, 2023-01.
HRC Imputation panel the Haplotype Reference Consortium. "A reference panel of 64,976 haplotypes for genotype imputation". Nature genetics, 2016, 48(10): 1279-1283.
RESHAPE Imputation panel Cavinato, T., Rubinacci, S., Malaspinas, A. S., & Delaneau, O. (2023). A resampling-based approach to share reference panels. bioRxiv, 2023-04.
South and East Asian Reference Database (SEAD) reference panel Imputation panel Yang, M. Y., Zhong, J. D., Li, X., Bai, W. Y., Yuan, C. D., Qiu, M. C., ... & Zheng, H. F. (2023). SEAD: an augmented reference panel with 22,134 haplotypes boosts the rare variants imputation and GWAS analysis in Asian population. medRxiv, 2023-12.
TOPMED Imputation panel Taliun, Daniel, et al. "Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program." Nature 590.7845 (2021): 290-299.
CNGB Imputation Service Imputation server Yu, C., Lan, X., Tao, Y., Guo, Y., Sun, D., Qian, P., ... & Li, L. (2022). A High-resolution Haplotype-resolved Reference Panel Constructed from the China Kadoorie Biobank Study. medRxiv, 2022-12.
Michigan Imputation server Das, Sayantan, et al. "Next-generation genotype imputation service and methods." Nature genetics 48.10 (2016): 1284-1287.
NyuWa Imputation server Zhang, P., Luo, H., Li, Y., Wang, Y., Wang, J., Zheng, Y., ... & Han100K Initiative. (2021). NyuWa Genome resource: a deep whole-genome sequencing-based variation profile and reference panel for the Chinese population. Cell Reports, 37(7), 110017.
Sanger Imputation server "A reference panel of 64,976 haplotypes for genotype imputation." Nature genetics 48, no. 10 (2016): 1279-1283.
TOPMED Imputation server Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., ... & Stilp, A. M. (2021). Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature, 590(7845), 290-299.
Westlake Imputation server Cong, P. K., Bai, W. Y., Li, J. C., Yang, M. Y., Khederzadeh, S., Gai, S. R., ... & Zheng, H. F. (2022). Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project. Nature Communications, 13(1), 1-15.
BEAGLE Phasing & Imputation tool (beagle) Browning, Sharon R., and Brian L. Browning. "Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering." The American Journal of Human Genetics 81.5 (2007): 1084-1097.

(beagle 4.1)Browning, Brian L., and Sharon R. Browning. "Genotype imputation with millions of reference samples." The American Journal of Human Genetics 98.1 (2016): 116-126.

(beagle 5.4 phasing) Browning, Brian L., et al. "Fast two-stage phasing of large-scale sequence data." The American Journal of Human Genetics 108.10 (2021): 1880-1890.

(beagle 5.4 imputation) Browning, Brian L., Ying Zhou, and Sharon R. Browning. "A one-penny imputed genome from next-generation reference panels." The American Journal of Human Genetics 103.3 (2018): 338-348.
Eagle Phasing & Imputation tool (EAGLE1) Loh, Po-Ru, Pier Francesco Palamara, and Alkes L. Price. "Fast and accurate long-range phasing in a UK Biobank cohort." Nature genetics 48.7 (2016): 811-816.

(EAGLE2) Loh, Po-Ru, et al. "Reference-based phasing using the Haplotype Reference Consortium panel." Nature genetics 48.11 (2016): 1443-1448.
GLIMPSE Phasing & Imputation tool Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J., & Delaneau, O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nature Genetics, 53(1), 120-126.

(using GLIMPSE for ancient DNA) Sousa da Mota, B., Rubinacci, S., Cruz Dávalos, D. I., G. Amorim, C. E., Sikora, M., Johannsen, N. N., ... & Delaneau, O. (2023). Imputation of ancient human genomes. Nature Communications, 14(1), 3660.
IMPUTE Phasing & Imputation tool (IMPUTE) Marchini, Jonathan, et al. "A new multipoint method for genome-wide association studies by imputation of genotypes." Nature genetics 39.7 (2007): 906-913.

(IMPUTE2) Howie, Bryan N., Peter Donnelly, and Jonathan Marchini. "A flexible and accurate genotype imputation method for the next generation of genome-wide association studies." PLoS genetics 5.6 (2009): e1000529.

(IMPUTE4) Bycroft, Clare, et al. "The UK Biobank resource with deep phenotyping and genomic data." Nature 562.7726 (2018): 203-209.

(IMPUTE5) Rubinacci, Simone, Olivier Delaneau, and Jonathan Marchini. "Genotype imputation using the positional burrows wheeler transform." PLoS genetics 16.11 (2020): e1009049.
MACH / minimach Phasing & Imputation tool (MACH) Li, Yun, et al. "MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes." Genetic epidemiology 34.8 (2010): 816-834.

(pre-phasing, minimac) Howie, Bryan, et al. "Fast and accurate genotype imputation in genome-wide association studies through pre-phasing." Nature genetics 44.8 (2012): 955-959.

(minimac2) Fuchsberger, Christian, Gonçalo R. Abecasis, and David A. Hinds. "minimac2: faster genotype imputation." Bioinformatics 31.5 (2015): 782-784.

(minimac3) Das, Sayantan, et al. "Next-generation genotype imputation service and methods." Nature genetics 48.10 (2016): 1284-1287.
SHAPEIT Phasing & Imputation tool (SHAPEIT5) Hofmeister, R. J., Ribeiro, D. M., Rubinacci, S., & Delaneau, O. (2023). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nature Genetics, 55(7), 1243-1249.

(SHAPEIT5) Hofmeister, R. J., Ribeiro, D. M., Rubinacci, S., & Delaneau, O. (2022). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. bioRxiv, 2022-10.

(SHAPEIT4) Delaneau, Olivier, et al. "Accurate, scalable and integrative haplotype estimation." Nature communications 10.1 (2019): 1-10.

(SHAPEIT3) O'Connell, Jared, et al. "Haplotype estimation for biobank-scale data sets." Nature genetics 48.7 (2016): 817-820.

(SHAPEIT2) Delaneau, Olivier, Jean-Francois Zagury, and Jonathan Marchini. "Improved whole-chromosome phasing for disease and population genetic studies." Nature methods 10.1 (2013): 5-6.

(SHAPEIT1) Delaneau, Olivier, Jonathan Marchini, and Jean-François Zagury. "A linear complexity phasing method for thousands of genomes." Nature methods 9.2 (2012): 179-181.
fastPHASE Phasing & Imputation tool Scheet, Paul, and Matthew Stephens. "A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase." The American Journal of Human Genetics 78.4 (2006): 629-644.
Review-Das Review Das, Sayantan, Gonçalo R. Abecasis, and Brian L. Browning. "Genotype imputation from large reference panels." Annu Rev Genomics Hum Genet 19.1 (2018): 73-96.
Review-Li Review Li, Yun, et al. "Genotype imputation." Annual review of genomics and human genetics 10 (2009): 387.
Review-Marchini Review Marchini, Jonathan, and Bryan Howie. "Genotype imputation for genome-wide association studies." Nature Reviews Genetics 11.7 (2010): 499-511.
1KG SV imputation panel Structural variants imputation panel Noyvert, B., Erzurumluoglu, A. M., Drichel, D., Omland, S., Andlauer, T. F., Mueller, S., ... & Ding, Z. (2023). Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations. medRxiv, 2023-12.

Imputation panel

1000 Genomes

  • NAME : 1000 Genomes
  • CATEGORY : Imputation panel
  • CITATION : 1000 Genomes Project Consortium. "A global reference for human genetic variation." Nature 526.7571 (2015): 68.

HGDP+1kGP

  • NAME : HGDP+1kGP
  • CATEGORY : Imputation panel
  • URL : https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/#the-gnomad-hgdp-and-1000-genomes-callset
  • CITATION : Koenig, Z., Yohannes, M. T., Nkambule, L. L., Goodrich, J. K., Kim, H. A., Zhao, X., ... & Martin, A. R. (2023). A harmonized public resource of deeply sequenced diverse human genomes. bioRxiv, 2023-01.
  • FULL NAME : Human Genome Diversity Project + 1000 Genomes project
  • SHORT NAME : HGDP+1kGP

HRC

  • NAME : HRC
  • CATEGORY : Imputation panel
  • CITATION : the Haplotype Reference Consortium. "A reference panel of 64,976 haplotypes for genotype imputation". Nature genetics, 2016, 48(10): 1279-1283.

RESHAPE

  • NAME : RESHAPE
  • CATEGORY : Imputation panel
  • URL : https://github.com/TheoCavinato/RESHAPE
  • CITATION : Cavinato, T., Rubinacci, S., Malaspinas, A. S., & Delaneau, O. (2023). A resampling-based approach to share reference panels. bioRxiv, 2023-04.
  • FULL NAME : REcombine and Share HAPlotypEs
  • SHORT NAME : RESHAPE
  • DESCRIPTION : RESHAPE removes sample-level genetic information from a reference panel to create a synthetic reference panel. By providing it with a genetic map and the VCF/BCF of a reference panel, RESHAPE outputs a VCF/BCF of the same size where each haplotypes corresponds to a mosaic of the original haplotypes of the reference panel.

South and East Asian Reference Database (SEAD) reference panel

  • NAME : South and East Asian Reference Database (SEAD) reference panel
  • CATEGORY : Imputation panel
  • URL : https://imputationserver.westlake.edu.cn/
  • CITATION : Yang, M. Y., Zhong, J. D., Li, X., Bai, W. Y., Yuan, C. D., Qiu, M. C., ... & Zheng, H. F. (2023). SEAD: an augmented reference panel with 22,134 haplotypes boosts the rare variants imputation and GWAS analysis in Asian population. medRxiv, 2023-12.

TOPMED

  • NAME : TOPMED
  • CATEGORY : Imputation panel
  • CITATION : Taliun, Daniel, et al. "Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program." Nature 590.7845 (2021): 290-299.

Imputation server

CNGB Imputation Service

  • NAME : CNGB Imputation Service
  • CATEGORY : Imputation server
  • URL : https://db.cngb.org/imputation/
  • CITATION : Yu, C., Lan, X., Tao, Y., Guo, Y., Sun, D., Qian, P., ... & Li, L. (2022). A High-resolution Haplotype-resolved Reference Panel Constructed from the China Kadoorie Biobank Study. medRxiv, 2022-12.

Michigan

NyuWa

  • NAME : NyuWa
  • CATEGORY : Imputation server
  • URL : http://bigdata.ibp.ac.cn/refpanel/getstarted.php
  • CITATION : Zhang, P., Luo, H., Li, Y., Wang, Y., Wang, J., Zheng, Y., ... & Han100K Initiative. (2021). NyuWa Genome resource: a deep whole-genome sequencing-based variation profile and reference panel for the Chinese population. Cell Reports, 37(7), 110017.

Sanger

  • NAME : Sanger
  • CATEGORY : Imputation server
  • URL : https://imputation.sanger.ac.uk/
  • CITATION : "A reference panel of 64,976 haplotypes for genotype imputation." Nature genetics 48, no. 10 (2016): 1279-1283.

TOPMED

  • NAME : TOPMED
  • CATEGORY : Imputation server
  • URL : https://imputation.biodatacatalyst.nhlbi.nih.gov/#!
  • CITATION : Taliun, D., Harris, D. N., Kessler, M. D., Carlson, J., Szpiech, Z. A., Torres, R., ... & Stilp, A. M. (2021). Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature, 590(7845), 290-299.

Westlake

  • NAME : Westlake
  • CATEGORY : Imputation server
  • URL : https://imputationserver.westlake.edu.cn/
  • CITATION : Cong, P. K., Bai, W. Y., Li, J. C., Yang, M. Y., Khederzadeh, S., Gai, S. R., ... & Zheng, H. F. (2022). Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project. Nature Communications, 13(1), 1-15.

Phasing & Imputation tool

BEAGLE

  • NAME : BEAGLE
  • CATEGORY : Phasing & Imputation tool
  • URL : https://faculty.washington.edu/browning/beagle/beagle.html
  • CITATION : (beagle) Browning, Sharon R., and Brian L. Browning. "Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering." The American Journal of Human Genetics 81.5 (2007): 1084-1097. (beagle 4.1)Browning, Brian L., and Sharon R. Browning. "Genotype imputation with millions of reference samples." The American Journal of Human Genetics 98.1 (2016): 116-126. (beagle 5.4 phasing) Browning, Brian L., et al. "Fast two-stage phasing of large-scale sequence data." The American Journal of Human Genetics 108.10 (2021): 1880-1890. (beagle 5.4 imputation) Browning, Brian L., Ying Zhou, and Sharon R. Browning. "A one-penny imputed genome from next-generation reference panels." The American Journal of Human Genetics 103.3 (2018): 338-348.

Eagle

  • NAME : Eagle
  • CATEGORY : Phasing & Imputation tool
  • URL : https://alkesgroup.broadinstitute.org/Eagle/
  • CITATION : (EAGLE1) Loh, Po-Ru, Pier Francesco Palamara, and Alkes L. Price. "Fast and accurate long-range phasing in a UK Biobank cohort." Nature genetics 48.7 (2016): 811-816. (EAGLE2) Loh, Po-Ru, et al. "Reference-based phasing using the Haplotype Reference Consortium panel." Nature genetics 48.11 (2016): 1443-1448.

GLIMPSE

  • NAME : GLIMPSE
  • CATEGORY : Phasing & Imputation tool
  • URL : https://odelaneau.github.io/GLIMPSE/
  • CITATION : Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J., & Delaneau, O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nature Genetics, 53(1), 120-126. (using GLIMPSE for ancient DNA) Sousa da Mota, B., Rubinacci, S., Cruz Dávalos, D. I., G. Amorim, C. E., Sikora, M., Johannsen, N. N., ... & Delaneau, O. (2023). Imputation of ancient human genomes. Nature Communications, 14(1), 3660.
  • FULL NAME : Genotype Likelihoods IMputation and PhaSing mEthod
  • SHORT NAME : GLIMPSE
  • DESCRIPTION : GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.

IMPUTE

  • NAME : IMPUTE
  • CATEGORY : Phasing & Imputation tool
  • URL : https://jmarchini.org/software/
  • CITATION : (IMPUTE) Marchini, Jonathan, et al. "A new multipoint method for genome-wide association studies by imputation of genotypes." Nature genetics 39.7 (2007): 906-913. (IMPUTE2) Howie, Bryan N., Peter Donnelly, and Jonathan Marchini. "A flexible and accurate genotype imputation method for the next generation of genome-wide association studies." PLoS genetics 5.6 (2009): e1000529. (IMPUTE4) Bycroft, Clare, et al. "The UK Biobank resource with deep phenotyping and genomic data." Nature 562.7726 (2018): 203-209. (IMPUTE5) Rubinacci, Simone, Olivier Delaneau, and Jonathan Marchini. "Genotype imputation using the positional burrows wheeler transform." PLoS genetics 16.11 (2020): e1009049.

MACH / minimach

SHAPEIT

  • NAME : SHAPEIT
  • CATEGORY : Phasing & Imputation tool
  • URL : https://odelaneau.github.io/shapeit4/ https://jmarchini.org/shapeit3/ https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
  • CITATION : (SHAPEIT5) Hofmeister, R. J., Ribeiro, D. M., Rubinacci, S., & Delaneau, O. (2023). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nature Genetics, 55(7), 1243-1249. (SHAPEIT5) Hofmeister, R. J., Ribeiro, D. M., Rubinacci, S., & Delaneau, O. (2022). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. bioRxiv, 2022-10. (SHAPEIT4) Delaneau, Olivier, et al. "Accurate, scalable and integrative haplotype estimation." Nature communications 10.1 (2019): 1-10. (SHAPEIT3) O'Connell, Jared, et al. "Haplotype estimation for biobank-scale data sets." Nature genetics 48.7 (2016): 817-820. (SHAPEIT2) Delaneau, Olivier, Jean-Francois Zagury, and Jonathan Marchini. "Improved whole-chromosome phasing for disease and population genetic studies." Nature methods 10.1 (2013): 5-6. (SHAPEIT1) Delaneau, Olivier, Jonathan Marchini, and Jean-François Zagury. "A linear complexity phasing method for thousands of genomes." Nature methods 9.2 (2012): 179-181.

fastPHASE

  • NAME : fastPHASE
  • CATEGORY : Phasing & Imputation tool
  • URL : http://scheet.org/software.html
  • CITATION : Scheet, Paul, and Matthew Stephens. "A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase." The American Journal of Human Genetics 78.4 (2006): 629-644.

Review

Review-Das

  • NAME : Review-Das
  • CATEGORY : Review
  • CITATION : Das, Sayantan, Gonçalo R. Abecasis, and Brian L. Browning. "Genotype imputation from large reference panels." Annu Rev Genomics Hum Genet 19.1 (2018): 73-96.

Review-Li

  • NAME : Review-Li
  • CATEGORY : Review
  • CITATION : Li, Yun, et al. "Genotype imputation." Annual review of genomics and human genetics 10 (2009): 387.

Review-Marchini

  • NAME : Review-Marchini
  • CATEGORY : Review
  • CITATION : Marchini, Jonathan, and Bryan Howie. "Genotype imputation for genome-wide association studies." Nature Reviews Genetics 11.7 (2010): 499-511.

Structural variants imputation panel

1KG SV imputation panel

  • NAME : 1KG SV imputation panel
  • CATEGORY : Structural variants imputation panel
  • CITATION : Noyvert, B., Erzurumluoglu, A. M., Drichel, D., Omland, S., Andlauer, T. F., Mueller, S., ... & Ding, Z. (2023). Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations. medRxiv, 2023-12.
  • KEYWORDS : structural variants, long-read