Practical implications of imputations with large reference panels

Systematic assessment of imputation performance using the 1000 ...

... imputation practice. First, in a study of imputation accuracy, we ... To speed up whole-genome imputation from a large reference panel ...

Genotype Imputation from Large Reference Panels | Request PDF

(2018) . By allowing the reconstruction of haplotypes in a target individual at sites not directly assayed, imputation effects an increase in the statistical ...

Practical Issues in Imputation-Based Association Mapping - PLOS

We find that imputation-based methods can be robust to imputation accuracy and can improve power to detect associations, even when average imputation accuracy ...

Using multi-population reference panels with IMPUTE2

These public databases provide powerful reference panels for genotype imputation studies. In this context, one important question is how to choose a reference ...

Sample size, window size, reference choice, and untyped rate

To comprehensively evaluate the effects of study sample size and reference sample size on imputation quality, we con- ducted imputation for studies of large, ...

Guidelines for Practical Imputation with Stan? - Modeling

There are auxiliary variables that can be used to help impute missing values in the covariates of interest as well with similar properties of ...

Boosting variant calling performance using a high-quality reference ...

There was minimal impact of sample mode on imputation accuracy with larger, more diverse panels. However, our results demonstrate that applying multisample ...

Genotype Imputation from Large Reference Panels - OUCI

Only variants that were previously observed in a reference panel of sequenced individuals can be imputed. However, the rapid increase in the number of deeply ...

Genotype imputation and reference panel: a systematic evaluation ...

Here, 622 imputations were conducted with 394 customized reference panels for Han Chinese and European populations. Besides validating the fact that ...

Multiple Imputation with Massive Data: an Application to the Panel ...

Practical difficulties and our approaches to overcoming ... income information for household reference persons and partners (for a full list, see ...

Rapid, Reference-Free human genotype imputation with denoising ...

Standard statistical imputation approaches rely on the co-location of large whole-genome sequencing-based reference panels, powerful computing ...

A genotype imputation reference panel specific for native Southeast ...

The limited choice of reference panel may potentially limit the accuracy and power when imputing populations that are not represented, ...

An empirical evaluation of genotype imputation of ancient DNA

2, and again indicate that us- ing a larger phased reference panel and study sample size increases performance. The effects were particularly ...

Reconstruction of private genomes through reference-based ...

Our results show that genomes in imputation server reference panels can be vulnerable to reconstruction, implying that additional safeguards may ...

Opening the Black-box of Imputation Software to Study the Impact of ...

of use in practice, but it does help ... Efficient Phasing and Imputation of Low-Coverage Sequencing Data. Using Large Reference Panels.

Custom Reference panel creation for data imputation from .vcf files

Yes, it is just a large VCF containing all variants called in the healthy controls or, to be more specific, the samples that you choose as your ...

Imputation and its importance in GWAS (Lecture 6) - YouTube

... imputation and its importance in GWAS. This lecture will cover the reference panels, file formats, algorithms and tools commonly used for ...

Comparison of genotype imputation strategies using a combined ...

However, the rate of increase of imputation accuracy clearly slowed down as reference panel size increased, especially for reference panels larger than 16. When ...

A Pipeline for Phasing and Genotype Imputation on Mixed Human ...

Iglesias, Haplotype reference consortium panel: Practical implications of imputations with large reference panels, Hum. Mutat., № 38, с. 1025 https://doi ...

Rare Variants Imputation in Admixed Populations - Frontiers

Using these composite reference panels, a number of studies (Pei et al., 2010; Howie et al., 2012; Verma et al., 2014; Liu et al., 2015) have ...