Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data.

ABSTRACT: Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs a

SUBMITTER: Kobayashi M 

PROVIDER: S-EPMC5737671 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature