2024
DOI: 10.1101/2024.08.11.607269
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Genotyping sequence-resolved copy-number variations using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes

Walfred Ma,
Mark JP Chaisson

Abstract: Genetic analysis of copy number variations (CNVs), especially in complex regions, is challenging due to reference bias and ambiguous alignment of Next-Generation Sequencing (NGS) reads to repetitive DNA. Consequently, aggregate copy numbers are typically analyzed, overlooking variation between gene copies.Pangenomes contain diverse sequences of gene copies and enable the study of sequence-resolved CNVs. We developed a method, ctyper, to discover sequence-resolved CNVs in NGS data by leveraging CNV genes from p… Show more

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