====== Genotype batches & pre-QC info ======

===== From deCODE to TSD =====

Genomic DNA from all study participants is extracted from peripheral whole blood and genotyped at deCODE genetics (Reykjavik, Iceland) on Illumina platforms (mostly Human OmniExpress-12v-1-1_B and Human OmniExpress-12v1_H, Illumina, San Diego, CA, USA), but also Global Screening Array from 2018 see [[https://docs.google.com/spreadsheets/d/1cJ1Ri7-FJisSQ3vBSJvgZNlmlx_z-xbB2x3KZ8mxQqA/edit?usp=sharing
|here]]) in accordance with the manufacturer’s standard protocol involving GenomeStudio software V2011.1 version 1.9.4.

Raw CIF (idat) intensity files from deCODE genetics are received and stored on hard drives in Thomas Bjella's and Lavinia Athanasiu's offices. These data will also be backed up onto TSD.

Chip fluorescence intensities are converted into genotypes with GenomeStudio by Lavinia Athanasiu to produce PLINK .bed, .bim, .fam file triplets.

For each set of data received from deCODE, a corresponding Genome Studio (Illumina) project is created.
The genotypes in PLINK format are exported thereafter. A preliminary gender estimate is also performed in Genome Studio.

The current pre-imputation PLINK QC and imputation procedures were designed by Francesco Bettella. The full procedures are documented [[genotype_imputation_protocol|here]].

Chip genotypes are stored on TSD under ''/cluster/project/p33/groups/biostat/genetics/rawdata/genotypes/preQC''.


===== Batch information =====

More information on the chip-genotyping of each batch can be found [[https://docs.google.com/spreadsheets/d/1cJ1Ri7-FJisSQ3vBSJvgZNlmlx_z-xbB2x3KZ8mxQqA/edit?usp=sharing|here]].

  * FHI_TOP95

  * LBD_rujescu

See also [[TSD directory structure]].