SNP Analysis practical

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[edit] SNP Analysis Practice

What is Haplotype Inference?
There are two copies of each chromosome in a diploid organism. Haplotype is data from a single copy. However, through the genotyping experiments, we can only get genotype which is mixed data from both chromosome copies. So, haplotype inference is infering haplotypes from genotype data.



PHASE

Implements a Bayesian statistical method for reconstructing haplotypes from population genotype data
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  • PHASE Homepage
  • Program Download
      - For Linux
      - For Windows
  • Sample file Download
      - test.inp
      - test2.inp
  • Documention (pdf)

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    Haploview is designed to simplify and expedite the process of haplotype analysis

    - examine block structures
    - generate haplotypes in these blocks
    - run association tests
    - save the data in a number of formats
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  • Haploview Homepage
  • Program Download
      - For Linux
      - For Windows
      -
  • Sample file Download
      - sample.ped
      - sample.info
  • Documention (pdf)

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  • SNPflank
  • Hardy-Weinberg Equilibrium Test
  • Functional Element SNPs Database (FESD)

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  • Java Runtime Environment
  • EditPlus Evaluation version
  • Lecture file


    • Retrieved from "http://www.koreanbio.org/Biocourse/index.php/SNP_Analysis_practical"
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