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COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.

Genome biology - 8 Sept 2026

Bolognini Davide, Guarracino Andrea, Paleni Chiara, Dudley Thomas S, Iacoviello Licia, Raveane Alessandro, Sudmant Peter H, Garrison Erik, Soranzo Nicole

Abstract excerpt

Pangenome graphs capture extensive structural diversity, but resolving complex loci from shallow sequencing remains challenging, particularly when samples are of low quality such as in ancient DNA. We introduce COSIGT (COsine SImilarity-based GenoTyper), which assigns diploid genotypes by matching read-depth distributions to haplotype paths via cosine similarity. Because this metric evaluates relative coverage...

Read the complete abstract on PubMed

Topics

Humans
Genotyping Techniques
Sequence Analysis, DNA
Genotype
Genetics, Population
Haplotypes

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Identifiers

PMID: 42711702
DOI: 10.1186/s13059-026-04242-4
PMCID: PMC13551797

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