SnpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.

ABSTRACT: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Software incompatibilities, and inconsistencies across computing environments, are recurrent challenges, leading to poor reproducibility. Existing semi-automated or automated solutions lack comprehensive quality checks, flexible workflow architecture, and user control. To address these challenges, we have developed snpQT: a scalable, stand-alone software pipeline using nextflow and BioContainers, for comprehensive, reproducible and interactive quality control of human genomic data. snpQT offers some 36 discrete quality filters or correction steps in a complete standardised pipeline, producing

SUBMITTER: Vasilopoulou C 

PROVIDER: S-EPMC8637247 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature