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HapTree-X: An Integrative Bayesian Framework for Haplotype Reconstruction from Transcriptome and Genome Sequencing Data

  • Emily Berger
  • Deniz Yorukoglu
  • Bonnie BergerEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

By running standard genotype calling tools, it is possible to accurately identify the number of “wild type” and “mutant” alleles for each single-nucleotide polymorphism (SNP) site. However, in the case of two heterozygous SNP sites, genotype calling tools cannot determine whether “mutant” alleles from different SNP loci are on the same chromosome or on different homologous chromosomes (i.e. compound heterozygote).

References

  1. 1.
    Bansal, V., Bafna, V.: Hapcut: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24(16), i153–i159 (2008)CrossRefGoogle Scholar
  2. 2.
    Berger, E., Yorukoglu, D., Peng, J., Berger, B.: Haptree: A novel Bayesian framework for single individual polyplotyping using NGS data. PLoS Computational Biology 10(3), e1003502 (2014)CrossRefGoogle Scholar
  3. 3.
    Serre, D., Gurd, S., Ge, B., Sladek, R., Sinnett, D., Harmsen, E., Bibikova, M., Chudin, E., Barker, D.L., Dickinson, T., et al.: Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genetics 4(2), e1000006 (2008)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Emily Berger
    • 1
    • 2
    • 3
  • Deniz Yorukoglu
    • 2
  • Bonnie Berger
    • 1
    • 2
    Email author
  1. 1.Department of MathematicsMITCambridgeUSA
  2. 2.Computer Science and Artificial Intelligence LaboratoryMITCambridgeUSA
  3. 3.Department of MathematicsUC BerkeleyBerkeleyUSA

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