The final data set produced by the 1000 Genomes Project was the phase 3 integrated data set. This contains fully phased haplotypes for 2,504 individuals. Full details can be found in the 1000 Genomes project phase 3 publication.
The developers of Beagle, Mach and Impute2 have all created data sets based on the 1000 Genomes data to use for imputation.
Please look at the software’s website to find those files.
Our released genotypes are created not just using sequence evidence but also imputation. If an individual has no coverage at a particular location but overall we have been able to determine there is variation at that location then we can statistically infer the genotype for that variant in that individual using haplotype information. This means we are able to provide complete haplotypes for all the variation we discover. For more information about how the genotype calling was done please refer to our phase 1 publication.
As the majority of sites in the genome only has only been sequenced to low coverage, in all our individuals some sites genotypes will be based on imputation.
The process used to create our genotypes first gave our merged sites and genotype likelihoods sets to Beagle to generate initial haplotypes (using 50 interations across all samples) and these were refined using a modified version of Thunder (it used 300 states chosen by longest matching haplotype at each iteration in addition to 100 randomly chosen states).
This process means we are unable to precisely identify which sites used imputation to generate their genotype. Without this process the approximate error rate for our heterozygous sites would be 20% so you can estimate that 20% of our heterozgous sites will have been changed on the basis of imputation. The sites covered by our exome sequencing represent our highest accuracy sites and these are the least likely to have been changed by this process. The converse is also true any site without any sequence alignment will have been imputed. You can find the depth of coverage at any site using our bam files. Other sites may have been given greater evidence on the basis of the imputation and refinement process.
You can find out more about this in our Phase 1 paper.