Working with PLINK2 fields on UKB-RAP

DRAGEN population level WGS variant data will be available in PLINK2 format. The psam files do not have a Phenotype column. To work with the PLINK2 data using plink2 add the  --no-pheno  parameter.

ie: plink2 --pfile ukb24308_cX_b0_v1  --check-sex --no-pheno --out outfile

Otherwise this will cause the following error:

Error: Line 1 of ukb24308_c#_b0_v1.psam has fewer tokens than expected.

Alternatively it is possible for researchers to add custom phenotypic column data using information fitting to their research question.

The data in field 24308 is the PLINK2 format of the ML-corrected pVCFs in field 24311. The smaller size of the PLINK2 data should aid researchers working with large numbers of SNPs and participants. Field 24309 is the BGEN format of this data.