This file describes MoBa 98K batch, located on TSD p697 project.

Plink bfile location

/cluster/projects/p697/genotype/MoBa_98k_post-imputationQC

The file hard-calls information forN=86890 individuals and M=5003746 markers.

A copy of the bim, fam and covariate files are also located at

/tsd/p697/data/durable/genotype/MoBa_98k_post-imputationQC/

Dosage data location

Dosage data in .bgen format is located here:

/cluster/projects/p697/genotype/MoBa_98k_post-imputationQC/bgen
/tsd/p697/data/durable/genotype/MoBa_98k_post-imputationQC/bgen

Corresponding .sample file has invalid FID column, simply a copy of IID column. If you use information on family structure, please use the data from .fam files.

Covariate file

98k-ec-eur-fin-batch-basic-qc-cov.txt hopefully contains a lot of the relevant infromation needed to link the genotypes to phenotypes, and to run analyses witht he relevant covariates, including principal components. (information on principal components is also available in a separate file 98k-ec-eur-fin-projections.txt).

NB: There are significant genotyping plate, genotyping batch, and imputation batch effects. Therefore, we highly recommend including these as covarates in all analyses. The ID_2445 column contains the F_ID_2445 for fathers, the M_ID_2445 for mothers, and the PREG_ID_BARN_NR for children (created using the command paste(child$PREG_ID, child$BARN_NR, sep="_") in R).

The FID and IID columns match the FID (column 1) and IID (column 2) of the plink fam file.

Any column with _num at the end of the column name contains a numeric version of the column with the same name (e.g., genotyping_center and genotyping_center_num).

There are some MZ twin pairs and across generation first degree relationships. Basic information about these relationships can be found in /tsd/p697/data/durable/projects/moba_qc_imputation/resources folder. Files: MZ_twin_pairs_identified_by_KING.txt and Within_generation_PO_across_generation_S_identified_by_KING.txt.