A comparative analysis of current phasing and imputation software
Whole-genome data has become significantly more accessible over the last two decades.
This can largely be attributed to both reduced sequencing costs and imputation models …
This can largely be attributed to both reduced sequencing costs and imputation models …
Molgenis-impute: imputation pipeline in a box
Background Genotype imputation is an important procedure in current genomic analysis
such as genome-wide association studies, meta-analyses and fine mapping. Although high …
such as genome-wide association studies, meta-analyses and fine mapping. Although high …
Assessment of imputation quality: comparison of phasing and imputation algorithms in real data
Despite the widespread use of genotype imputation tools and the availability of different
approaches, late developments of currently used programs have not been compared …
approaches, late developments of currently used programs have not been compared …
Evaluating imputation algorithms for low-depth genotyping-by-sequencing (GBS) data
AW Chan, MT Hamblin, JL Jannink - PLoS One, 2016 - journals.plos.org
Well-powered genomic studies require genome-wide marker coverage across many
individuals. For non-model species with few genomic resources, high-throughput …
individuals. For non-model species with few genomic resources, high-throughput …
On combining reference data to improve imputation accuracy
Genotype imputation is an important tool in human genetics studies, which uses reference
sets with known genotypes and prior knowledge on linkage disequilibrium and …
sets with known genotypes and prior knowledge on linkage disequilibrium and …
GeneImp: fast imputation to large reference panels using genotype likelihoods from ultralow coverage sequencing
A Spiliopoulou, M Colombo, P Orchard, F Agakov… - Genetics, 2017 - academic.oup.com
We address the task of genotype imputation to a dense reference panel given genotype
likelihoods computed from ultralow coverage sequencing as inputs. In this setting, the data …
likelihoods computed from ultralow coverage sequencing as inputs. In this setting, the data …
minimac2: faster genotype imputation
Genotype imputation is a key step in the analysis of genome-wide association studies.
Upcoming very large reference panels, such as those from The 1000 Genomes Project and …
Upcoming very large reference panels, such as those from The 1000 Genomes Project and …
genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools
LP Lemieux Perreault, MA Legault, G Asselin… - …, 2016 - academic.oup.com
Genotype imputation is now commonly performed following genome-wide genotyping
experiments. Imputation increases the density of analyzed genotypes in the dataset …
experiments. Imputation increases the density of analyzed genotypes in the dataset …
A new statistic to evaluate imputation reliability
P Lin, SM Hartz, Z Zhang, SF Saccone, J Wang… - PloS one, 2010 - journals.plos.org
Background As the amount of data from genome wide association studies grows
dramatically, many interesting scientific questions require imputation to combine or expand …
dramatically, many interesting scientific questions require imputation to combine or expand …
Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data
Background Genome imputation, admixture resolution and genome-wide association
analyses are timely and computationally intensive processes with many composite and …
analyses are timely and computationally intensive processes with many composite and …