Genotype and SNP calling from next-generation sequencing data

TY - JOUR

T1 - Genotype and SNP calling from next-generation sequencing data

AU - Nielsen, Rasmus

AU - Paul, Joshua S.

AU - Albrechtsen, Anders

AU - Song, Yun S.

PY - 2011/6

Y1 - 2011/6

N2 - Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.

AB - Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.

KW - Alleles

KW - Chromosome Mapping

KW - Data Interpretation, Statistical

KW - Genetic Diseases, Inborn

KW - Genotype

KW - Humans

KW - Likelihood Functions

KW - Linkage Disequilibrium

KW - Polymorphism, Single Nucleotide

KW - Probability

KW - Sequence Analysis, DNA

U2 - 10.1038/nrg2986

DO - 10.1038/nrg2986

M3 - Review

C2 - 21587300

SN - 1471-0056

VL - 12

SP - 443

EP - 451

JO - Nature Reviews. Genetics

JF - Nature Reviews. Genetics

IS - 6

ER -