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The files here are used to run an automated workflow in GSK's global data center (GDC) making use of the wrappered SGE (abq) to:

1. QC and reformat the directly assayed array genotypes producing reports for review
2. Phase results from (1) using either MACH if < 1,000 samples or hapi-ur if > 1,000 samples
3. Impute using the 1000 Genomes Phase 1 reference haplotypes into the results from (2) with minimac

Click on each of the above for details or click here for guidance on how to run.