Quality control for 1000 Genomes

We performed standard quality control analysis on the 1000 Genomes Project genotypes that were generated on the Illumina Omni2.5M chip, at the Broad and Sanger Institutes.

report on the quality steps performed (Acrobat file)
table of quality statistics per SNP and [readme] (Text files)
table of quality statistics per sample and [readme] (Text files)
PLINK binary format files of independent samples (Tar.gz file 295.19 MB)
and high quality SNPs [readme] (Text file)
PLINK binary format files with the reconstructed pedigrees, (Tar.gz file 410.4 MB)
including dummy individuals needed to link the genotyped samples, high quality SNPs only [readme] (Text file)
marker map file (PLINK .bim format) of 57,984 SNPs used in principal components analysis, GRCh37/hg19

If you use these files, please cite the 1000 Genomes Project, as well as Roslin NM, Li W, Paterson AD, Strug LJ. Quality control analysis of the 1000 Genomes Project Omni2.5 genotypes (Abstract/Program #576/F). Presented at the 66th Annual Meeting of The American Society of Human Genetics, October 18-22, 2016, Vancouver, Canada.