Reveel: large-scale population genotyping using low-coverage sequencing data

BioRxiv : the Preprint Server for Biology
Lin HuangSerafim Batzoglou

Abstract

Population low-coverage whole-genome sequencing is rapidly emerging as a prominent approach for discovering genomic variation and genotyping a cohort. This approach combines substantially lower cost than full-coverage sequencing with whole-genome discovery of low-allele-frequency variants, to an extent that is not possible with array genotyping or exome sequencing. However, a challenging computational problem arises when attempting to discover variants and genotype the entire cohort. Variant discovery and genotyping are relatively straightforward on a single individual that has been sequenced at high coverage, because the inference decomposes into the independent genotyping of each genomic position for which a sufficient number of confidently mapped reads are available. However, in cases where low-coverage population data are given, the joint inference requires leveraging the complex linkage disequilibrium patterns in the cohort to compensate for sparse and missing data in each individual. The potentially massive computation time for such inference, as well as the missing data that confound low-frequency allele discovery, need to be overcome for this approach to become practical. Here, we present Reveel, a novel method for sing...Continue Reading

Related Concepts

Alleles
Base Sequence
Genome
Joints
Patterns
Cohort
Gene Mutant
Simulation
Drug Discovery
Population Group

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