General Information
| Description | Haplotyping and genotype imputation on graphics processing units |
| Homepage | http://code.google.com/p/mendel-gpu/ |
Publications
Mendel-GPU: haplotyping and genotype imputation on graphics processing units
Motivation:
In modern sequencing studies, one can improve the confidence of genotype calls by phasing haplotypes using information from an external reference panel of fully typed unrelated individuals. However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data.
Results:
Our graphics processing unit based software delivers haplotyping and imputation accuracies comparable to competing programs at a fraction of the computational cost and peak memory demand.
Availability:
Mendel-GPU, our OpenCL software, runs on Linux platforms and is portable across AMD and nVidia GPUs. Users can download both code and documentation at http://code.google.com/p/mendel-gpu/.
Contact:
gary.k.chen@usc.edu
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
FISH
Published March 2014
Fast and accurate diploid genotype imputation via segmental hidden Markov model
DISTMIX
Published June 2015
Direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts
H-PoP and H-PoPG
Published August 2016
Heuristic partitioning algorithms for single individual haplotyping of polyploids
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
