The exome sequencing the 1000 Genomes project has undertaken is targetting the entirety of the CCDS gene set.
The targets used for the phase 1 data release of 1092 samples can be found in technical/reference/exome_pull_down_targets_phases1_and_2; the targets for phase 3 analysis can be found in technical/reference/exome_pull_down_targets/.
The phase 1 and 2 targets are intersections of the different technologies used and the CCDS gene list. For phase 3 we are using a union of two different pull-down lists: NimbleGen EZ_exome v1 and Agilent sure select v2
In phase 3 very little exome specific calling took place. Instead analysis groups called variants tending to use the low coverage and exome data together in an integrated manner.