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
- NAME : Michigan
- CATEGORY : Imputation server
- URL : https://imputationserver.sph.umich.edu/index.html#! https://imputationserver.readthedocs.io/en/latest/
- CITATION : Das, Sayantan, et al. "Next-generation genotype imputation service and methods." Nature genetics 48.10 (2016): 1284-1287.
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
- NAME : MACH / minimach
- CATEGORY : Phasing & Imputation tool
- URL : http://csg.sph.umich.edu/abecasis/MaCH/index.html https://genome.sph.umich.edu/wiki/Minimac https://genome.sph.umich.edu/wiki/Minimac2 https://genome.sph.umich.edu/wiki/Minimac3 https://genome.sph.umich.edu/wiki/Minimac4
- CITATION : (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
- 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