Generation and Utilization of Quality Control Set 90pct10dp on OQFE Data

Single unfiltered multi-sample VCF files were provided for all UK Biobank whole exome sequencing (WES) releases (200k, 300k, 450k, and the final exome release). To aid researchers to generate a quality control data set for genotype-phenotype association analyses, a “90pct10dp” QC filter was applied to all UK Biobank aggregate data sets based on analyses on the UK Biobank 200k data release.

Only variant sites with at least 90% of the genotypes having DP>10 were retained by this filter. The filtered data sets are provided in the “helper_files” folders of all UK Biobank WES releases. For details on the analysis and other considerations, please refer to the UKB-RAP documentation: "Details on Processing Whole Exome Datasets to Generate the Quality Control Set".