Genotyping process and sample QC - Genotypes - Genomics
DescriptionInformation from the genotype calling and sample quality control pipeline, such as relatedness and population structure (PCA), which may be important for downstream analyses. Category also includes experimental factors from the Affymetrix genotype calling pipeline.
These fields are a subset of the sample quality control information available in the sample_qc file (which can be downloaded from the EGA). Descriptions of all the Sample-QC fields are in Resource 531.
Information on estimated relatedness can be obtained using the ukbgene utility - see Resource 664.