Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks.

ABSTRACT: High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing genotyping technologies when resources are limited. In this work, we are proposing a new imputation pipeline ("HBimpute") that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and subsequently use the reads of all locally similar lines in the variant calling for a specific line. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European m

SUBMITTER: Pook T 

PROVIDER: S-EPMC8699914 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature