Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.

ABSTRACT: Accurate characterization of genetic variation is fundamental to genomics. While long-read sequencing technologies promise to resolve complex genomic regions and improve variant detection, their application in complex genomes has not been well validated. Here, we systematically investigate the factors influencing variant calling accuracy using accurate long reads. Using human trio data with known variants to simulate variable ploidy levels (diploid, tetraploid, hexaploid), we demonstrate that while variant sites can often be identified accurately, genotyping accuracy decreases with increasing ploidy due to allelic dosage uncertainty. This highlights a specific challenge in assigning correct allele counts in polyploids even with high depth, separate from the initial variant discovery. We th

SUBMITTER: Fukasawa Y 

PROVIDER: S-EPMC12809965 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature