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findhap.f90

findhap.f90

findhap.f90 is a tool for genotype imputation and haplotype detection. The findhap.f90 algorithm uses allele read counts to improve imputation accuracy. The Authors claim the findhap.f90 to be more accurate than Beagle (v4) and up 400 times faster.

Topic

Population genetics

Details

  • Operation: Phasing; Imputation
  • Software interface: Command-line user interface
  • Language: Fortran
  • Operating system: Linux
  • License: Public domain
  • Cost: Free
  • Version name: 4 | 3 | 2
  • Maturity: beta
  • Credit: the Agricultural Research Service, United States Department of Agriculture, the National Association of Animal Breeders, the University of Maryland School of Medicine, Agricultural Research Service U.S. Department of Agriculture.
  • Contact: Paul M. VanRaden Paul.VanRaden _at_ ars.usda.gov | Chuanyu Sun CSun _at_ sexingtechnologies.com | Jeffrey R. OConnell joconnel _at_ medicine.umaryland.edu
  • Collection: -

Publications

VanRaden PM, Sun C, O'Connell JR "Fast imputation using medium or low-coverage sequence data." BMC Genet. 2015 Jul 14;16:82. https://doi.org/10.1186/s12863-015-0243-7
PMID: 26168789
PMCID: PMC4501077

VanRaden PM, O'Connell JR, Wiggans GR, Weigel KA "Genomic evaluations with many more genotypes." Genet Sel Evol. 2011 Mar 2;43:10. https://doi.org/10.1186/1297-9686-43-10
PMID: 21366914
PMCID: PMC3056758

VanRaden PM, Null DJ, Sargolzaei M, Wiggans GR, Tooker ME, Cole JB, Sonstegard TS, Connor EE, Winters M, van Kaam JB, Valentini A, Van Doormaal BJ, Faust MA, Doak GA "Genomic imputation and evaluation using high-density Holstein genotypes." J Dairy Sci. 2013 Jan;96(1):668-78. https://doi.org/10.3168/jds.2012-5702
PMID: 23063157

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