Varigraph: An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes.

Abstract excerpt

Accurate variant genotyping is crucial for genomics-assisted breeding. Graph pangenome references can address single-reference bias, thereby enhancing the performance of variant genotyping and empowering downstream applications in population genetics and quantitative genetics. However, existing pangenome-based genotyping methods are ineffective in handling large or complex pangenome graphs, particularly in...

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