منابع مشابه
Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis.
Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due t...
متن کاملHaplotype frequency estimation in the presence of genotyping errors.
Several statistical methods have been proposed to estimate haplotype frequencies, either based on unrelated individuals or based on families. These estimates may yield insights on population genetics as well as associations between candidate regions and disease of interest. One limitation of the existing methods is that all these methods make the implicit assumption that there are no genotyping...
متن کاملIncorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms.
The accuracy of the vast amount of genotypic information generated by high-throughput genotyping technologies is crucial in haplotype analyses and linkage-disequilibrium mapping for complex diseases. To date, most automated programs lack quality measures for the allele calls; therefore, human interventions, which are both labor intensive and error prone, have to be performed. Here, we propose a...
متن کاملEfficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids
The problem of genotyping polyploids is extremely important for the creation of genetic maps and assembly of complex plant genomes. Despite its significance, polyploid genotyping still remains largely unsolved and suffers from a lack of statistical formality. In this paper a graphical bayesian model for SNP genotyping data is introduced. This model can infer genotypes even when the ploidy of th...
متن کاملSNP genotyping and parameter estimation in polyploids using low-coverage sequencing data
Motivation Genotyping and parameter estimation using high throughput sequencing data are everyday tasks for population geneticists, but methods developed for diploids are typically not applicable to polyploid taxa. This is due to their duplicated chromosomes, as well as the complex patterns of allelic exchange that often accompany whole genome duplication (WGD) events. For WGDs within a single ...
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ژورنال
عنوان ژورنال: Frontiers in Plant Science
سال: 2018
ISSN: 1664-462X
DOI: 10.3389/fpls.2018.00564