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bioRxiv · 10.1101/2021.12.03.471074

KAGE: Fast alignment-free graph-based genotyping of SNPs and short indels

Grytten, I.·Rand, K. D.·Sandve, G. K.
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Abstract

Genotyping is a core application of high-throughput sequencing. We present KAGE, a genotyper for SNPs and short indels that is inspired by recent developments within graph-based genome representations and alignment-free methods. KAGE uses a pan-genome representation of the population to efficiently and accurately predict genotypes. Two novel ideas improve both the speed and accuracy: a Bayesian model incorporates genotypes from thousands of individuals to improve prediction accuracy, and a computationally efficient method leverages correlation between variants. We show that the accuracy of KAGE is at par with the best existing alignment-free genotypers, while being an order of magnitude faster.

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Grytten, I., Rand, K. D., Sandve, G. K.. 2021-12-05. KAGE: Fast alignment-free graph-based genotyping of SNPs and short indels. https://doi.org/10.1101/2021.12.03.471074

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