The sample data for the project has been collected in rounds so not all the samples were available from the start of the project.
The pilot studies referred to different strategies of sequencing but the full project phases refer to sets of samples. All the samples in all the phases will be sequenced both using whole genome low coverage and full exome high coverage aswell as genotyped on at least one high density genotyping platform.
Phase 1 contains slightly more than 1000 individuals and phase 2 will have nearly 1600 individuals (this does include then 1000 from phase 1).
By demarcating the analysis process this way we are able to apply any lessons we learn in one phase to the next phase hence the change in reference sequence for mapping between phase 1 and phase 2