1000 Genomes Phase 1 Analysis

Variant discovery and individual genotypes for 1092 individuals from the 1000 Genomes Project Phase 1 data release. Site discovery and genotyping for SNPs are based on both low coverage and exome capture sequence data for short indels, only low coverage data, and for large deletions, only the 946 individuals with Illumina low coverage sequence data are used. As a final step, statistical genotype imputation using the linkage disequilibrium between nearby sites refines the individual genotypes and merges information from all three variant types.