Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

ABSTRACT:

Background

Genotyping of sequence variants typically involves, as a first step, the alignment of sequencing reads to a linear reference genome. Because a linear reference genome represents only a small fraction of all the DNA sequence variation within a species, reference allele bias may occur at highly polymorphic or divergent regions of the genome. Graph-based methods facilitate the comparison of sequencing reads to a variation-aware genome graph, which incorporates a collection of non-redundant DNA sequences that segregate within a species. We compared the accuracy and sensitivity of graph-based sequence variant genotyping using the Graphtyper software to two widely-used methods, i.e., GATK and SAMtools, which rely on linear reference genomes using whole-genome sequencing data f

SUBMITTER: Crysnanto D 

PROVIDER: S-EPMC6521551 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature