Haplotype Estimation Using Sequencing Reads

作者: Olivier Delaneau , Bryan Howie , Anthony J. Cox , Jean-François Zagury , Jonathan Marchini

DOI: 10.1016/J.AJHG.2013.09.002

关键词: Computational biologyDeep sequencing1000 Genomes ProjectData sequencesWord error rateHaplotypeBiologySequence (medicine)GeneticsBase (topology)Haplotype estimation

摘要: … when we considered all heterozygous genotypes in the samples… in the BAM files and identify those that span at least two … of 300 bp, 500 bp and 1,000 bp mean insert sizes. We also tried …

参考文章(18)
Silviu-Alin Bacanu, Testing for modes of inheritance involving compound heterozygotes. Genetic Epidemiology. ,vol. 37, pp. 522- 528 ,(2013) , 10.1002/GEPI.21732
Olivier Delaneau, Jean-Francois Zagury, Jonathan Marchini, Improved whole-chromosome phasing for disease and population genetic studies Nature Methods. ,vol. 10, pp. 5- 6 ,(2013) , 10.1038/NMETH.2307
Sharon R. Browning, Brian L. Browning, Haplotype phasing: existing methods and new developments Nature Reviews Genetics. ,vol. 12, pp. 703- 714 ,(2011) , 10.1038/NRG3054
Bryan Howie, Jonathan Marchini, Matthew Stephens, Genotype Imputation with Thousands of Genomes G3: Genes, Genomes, Genetics. ,vol. 1, pp. 457- 470 ,(2011) , 10.1534/G3.111.001198
Ryan Tewhey, Vikas Bansal, Ali Torkamani, Eric J. Topol, Nicholas J. Schork, The importance of phase information for human genomics Nature Reviews Genetics. ,vol. 12, pp. 215- 223 ,(2011) , 10.1038/NRG2950
Brian L. Browning, Sharon R. Browning, A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals American Journal of Human Genetics. ,vol. 84, pp. 210- 223 ,(2009) , 10.1016/J.AJHG.2009.01.005
Grégory F Schneider, Cees Dekker, DNA sequencing with nanopores Nature Biotechnology. ,vol. 30, pp. 326- 328 ,(2012) , 10.1038/NBT.2181
Jonathan Marchini, Bryan Howie, Genotype imputation for genome-wide association studies Nature Reviews Genetics. ,vol. 11, pp. 499- 511 ,(2010) , 10.1038/NRG2796
Heng Li, Richard Durbin, None, Inference of human population history from individual whole-genome sequences Nature. ,vol. 475, pp. 493- 496 ,(2011) , 10.1038/NATURE10231