期刊
NATURE METHODS
卷 19, 期 6, 页码 705-+出版社
NATURE PORTFOLIO
DOI: 10.1038/s41592-022-01457-8
关键词
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资金
- Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health
- Indian Institute of Science
Approximately 5-10% of the human genome is inaccessible due to the presence of repetitive sequences. Existing long-read mappers often yield incorrect alignments and variant calls within repetitive sequences. To address this issue, a new long-read mapping method called Winnowmap2 was developed, which is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats.
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.
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