Evaluation of variant calling tools for large plant genome re-sequencing.

ABSTRACT:

Background

Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breeding, population diversity studies for eco-geographical adaption, genotyping crop germplasm collections, and others. Accurately detecting SNPs from large polyploid crop genomes such as wheat is crucial and challenging. A few variant calling methods have been previously developed but they show a low concordance between their variant calls. A gold standard of variant sets generated from one human individual sample was established for variant calling tool evaluations, however hitherto no gold standard of crop variant set is available for wheat use. The intent of this st

SUBMITTER: Yao Z 

PROVIDER: S-EPMC7430858 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature