Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads
نویسندگان
چکیده
منابع مشابه
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads
MOTIVATION Hidden Markov model, based on Li and Stephens model that takes into account chromosome sharing of multiple individuals, results in mainstream haplotype phasing algorithms for genotyping arrays and next-generation sequencing (NGS) data. However, existing methods based on this model assume that the allele count data are independently observed at individual sites and do not consider hap...
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MOTIVATION Given the current costs of next-generation sequencing, large studies carry out low-coverage sequencing followed by application of methods that leverage linkage disequilibrium to infer genotypes. We propose a novel method that assumes study samples are sequenced at low coverage and genotyped on a genome-wide microarray, as in the 1000 Genomes Project (1KGP). We assume polymorphic site...
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MOTIVATION Low coverage sequencing provides an economic strategy for whole genome sequencing. When sequencing a set of individuals, genotype calling can be challenging due to low sequencing coverage. Linkage disequilibrium (LD) based refinement of genotyping calling is essential to improve the accuracy. Current LD-based methods use read counts or genotype likelihoods at individual potential pol...
متن کاملSimultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.
We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype...
متن کاملAlgorithms for Haplotype Phasing
A haplotype is the sequence of nucleotides along a single chromosome. As humans, we have 23 pairs of chromosomes. However, with current technology, it is di cult to separate the two chromosomes of a pair and we often get combined haplotype, or genotype, information. The objective of haplotype phasing is to resolve (phase) the haplotypes given genotype information. Knowing the haplotypes not onl...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2013
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btt418