Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit.

ABSTRACT:

Background

Whole genome sequencing (WGS) is becoming increasingly prevalent for molecular diagnosis, staging and prognosis because of its declining costs and the ability to detect nearly all genes associated with a patient's disease. The currently widely accepted variant calling pipeline, GATK, is limited in terms of its computational speed and efficiency, which cannot meet the growing analysis needs.

Results

Here, we propose a fast and accurate DNASeq variant calling workflow that is purely composed of tools from LUSH toolkit. The precision and recall measurements indicate that both the LUSH and GATK pipelines exhibit high levels of consistency, with precision and recall rates exceeding 99% on the 30x NA12878 dataset. In terms of processing speed, the LUSH pipeline outperfo

SUBMITTER: Wang T 

PROVIDER: S-EPMC11465951 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature