Quality Control of the DRAGEN PLINK2 WGS

Youjie Zeng

Hi there, is there a quality control process in place before the PLINK files are generated? If so, what exact filters are applied during QC?

Also, are there any recommended additional QC steps that should be considered to better support downstream genetic association analyses?

Thank you very much!

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    Lucy BG The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Youjie,

    We have two articles on the DRAGEN datasets released which may assist you in understanding the steps taken to prepare the data, the filters applied, and how best to use it in your current workflow.

    The first article covers the gVCF, pVCF, and CRAM format files which were released in November 2023: Initial DRAGEN whole genome sequencing (WGS) data release

    The second article covers the ML-corrected pVCF, BGEN and PLINK2 format files which were released in March 2025: ML-Corrected DRAGEN whole genome sequencing (WGS) release

    Each article covers the respective pipeline and quality control steps which occurred to prepare the data for release. 

    Hope this helps!

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