Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.

Abstract excerpt

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 sites have been...

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