Accurate, scalable and integrative haplotype estimation
SIB Swiss Institute of Bioinformatics · University of Lausanne · +4 more institutions
Abstract
The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold…
Citation impact
- FWCI
- 42.10
- Percentile
- 100%
- References
- 32
Authors
5- ODOlivier DelaneauCorresponding
SIB Swiss Institute of Bioinformatics, University of Lausanne
- JZJean‐François Zagury
Conservatoire National des Arts et Métiers, HESAM Université
- MRMatthew R. Robinson
SIB Swiss Institute of Bioinformatics, University of Lausanne
- JMJonathan Marchini
University of Oxford
- ETEmmanouil T. Dermitzakis
University of Geneva, SIB Swiss Institute of Bioinformatics
Topics & keywords
- Haplotype
- Scalability
- Computer science
- Haplotype estimation
- Genome
- Computational biology
- Data mining
- Phaser