An accurate phasing tool via high-quality heterozygous variations

Zhang, J.; Nie, F.; Wang, J.

doi:10.64898/2025.12.21.695866

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bioRxiv · 10.64898/2025.12.21.695866

An accurate phasing tool via high-quality heterozygous variations

Zhang, J.·Nie, F.·Wang, J.

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Abstract

Long-read phasing has become a widely adopted approach for reconstructing paternal and maternal haplotypes in diploid genomes. However, most existing phasing methods treat all variants equally, even though low-quality variants frequently introduce switch errors. We present a new phasing method, snpphaser, which first phases high-quality variants and then leverages them to filter out low-quality variants that are inconsistent with the high-confidence haplotypes. We benchmarked snpphaser against state-of-the-art phasing methods across nine diverse datasets. The results demonstrate that snpphaser achieves superior contiguity and accuracy compared to existing approaches.

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Zhang, J., Nie, F., Wang, J.. 2025-12-23. An accurate phasing tool via high-quality heterozygous variations. https://doi.org/10.64898/2025.12.21.695866

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