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A sequence-aware merger of genomic structural variations at population scale

Author

Listed:
  • Zeyu Zheng

    (Lanzhou University)

  • Mingjia Zhu

    (Lanzhou University)

  • Jin Zhang

    (Lanzhou University)

  • Xinfeng Liu

    (Lanzhou University)

  • Liqiang Hou

    (Lanzhou University)

  • Wenyu Liu

    (Lanzhou University)

  • Shuai Yuan

    (Lanzhou University)

  • Changhong Luo

    (Lanzhou University)

  • Xinhao Yao

    (Lanzhou University)

  • Jianquan Liu

    (Lanzhou University)

  • Yongzhi Yang

    (Lanzhou University)

Abstract

Merging structural variations (SVs) at the population level presents a significant challenge, yet it is essential for conducting comprehensive genotypic analyses, especially in the era of pangenomics. Here, we introduce PanPop, a tool that utilizes an advanced sequence-aware SV merging algorithm to efficiently merge SVs of various types. We demonstrate that PanPop can merge and optimize the majority of multiallelic SVs into informative biallelic variants. We show its superior precision and lower rates of missing data compared to alternative software solutions. Our approach not only enables the filtering of SVs by leveraging multiple SV callers for enhanced accuracy but also facilitates the accurate merging of large-scale population SVs. These capabilities of PanPop will help to accelerate future SV-related studies.

Suggested Citation

  • Zeyu Zheng & Mingjia Zhu & Jin Zhang & Xinfeng Liu & Liqiang Hou & Wenyu Liu & Shuai Yuan & Changhong Luo & Xinhao Yao & Jianquan Liu & Yongzhi Yang, 2024. "A sequence-aware merger of genomic structural variations at population scale," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45244-9
    DOI: 10.1038/s41467-024-45244-9
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    References listed on IDEAS

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    1. Yong Zhou & Zhichao Yu & Dmytro Chebotarov & Kapeel Chougule & Zhenyuan Lu & Luis F. Rivera & Nagarajan Kathiresan & Noor Al-Bader & Nahed Mohammed & Aseel Alsantely & Saule Mussurova & João Santos & , 2023. "Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
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