PT  - JOURNAL ARTICLE
AU  - Donald Freed
AU  - Renke Pan
AU  - Haodong Chen
AU  - Zhipan Li
AU  - Jinnan Hu
AU  - Rafael Aldana
TI  - DNAscope: High accuracy small variant calling using machine learning
AID  - 10.1101/2022.05.20.492556
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.05.20.492556
4099  - http://biorxiv.org/content/early/2022/05/22/2022.05.20.492556.short
4100  - http://biorxiv.org/content/early/2022/05/22/2022.05.20.492556.full
AB  - We present DNAscope, an accurate and efficient germline small-variant caller. DNAscope combines the robust and well-established preprocessing and assembly mathematics of the GATK’s HaplotypeCaller with a machine-learned genotyping model. Benchmarks of DNAscope and DNAseq (Sentieon’s GATK-matching germline variant calling pipeline) demonstrate that DNAscope achieves superior SNP and insertion/deletion accuracy with reduced computational cost.Competing Interest StatementD.F., H.C., Z.L., J.H. and R.A. are current employees of Sentieon, Inc., and hold stock options as part of the standard compensation package. R.P. is former employee of Sentieon.