Read-based phasing of related individuals.
Read-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information-reads and pedigree-has the potential to deliver results better than each individually.



We provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2× for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15× coverage per individual.



https://bitbucket.org/whatshap/whatshap



t.marschall@mpi-inf.mpg.de.
Center for Bioinformatics, Saarland University, Saarbrücken, Germany Max Planck Institute for Informatics, Saarbrücken, Germany Saarbrücken Graduate School of Computer Science, Saarland University, Saarbrücken, Germany.
Shilpa
S
Garg
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-17121 Solna, Sweden.
Marcel
M
Martin
Center for Bioinformatics, Saarland University, Saarbrücken, Germany Max Planck Institute for Informatics, Saarbrücken, Germany.
Tobias
T
Marschall
D000465:Algorithms; D005838:Genotype; D006239:Haplotypes; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA