TY - JOUR T1 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling JF - bioRxiv DO - 10.1101/2021.12.29.474431 SP - 2021.12.29.474431 AU - Zhenxian Zheng AU - Shumin Li AU - Junhao Su AU - Amy Wing-Sze Leung AU - Tak-Wah Lam AU - Ruibang Luo Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/11/22/2021.12.29.474431.abstract N2 - Deep learning-based variant callers are becoming the standard and have achieved superior SNP calling performance using long reads. In this paper, we present Clair3, which leveraged the best of two major method categories: pile-up calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 ran faster than any of the other state-of-the-art variant callers and performed the best, especially at lower coverage.Competing Interest StatementR. L. receives research funding from ONT. The remaining authors declare no competing interests. ER -