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https-github.com-yangjl-phasing's Introduction

Imputation and Phasing

Simulation

  1. A function to simulate a group of parent-progeny genotyped via GBS with different het/hom error rate
SimSelfer(size.array=20, het.error=0.7, hom.error=0.002, numloci=1000, recombination=TRUE)
  1. Visualize object returned from SimSelfer.
plotpa(sim, kids=10, cols=c("red", "blue"), ...)

Evaluation

  1. imputation rate
  2. error rate (phasing and imputation)
  3. efficiency
  4. others

List of software to test

  1. ProgenyArray
  2. ENT
    • using mom + mom -> kid: imputation rate .85
    • paper
  3. reHC-*
  4. mpimpute, source code
  5. LinkImpute
  6. Haploscribe
  • Beagle trios
  • MACH
  • FIMPUTE
  • findhap.f90
  • PHASEBOOK
  • Alpha{Phase, Impute}
  • LDMIP
  • SHAPEIT

https-github.com-yangjl-phasing's People

Contributors

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Watchers

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