We evaluated the quality of the different sets of haplotypes by looking at the concordance of the inferred genotypes to validation sets of SNP and indel genotypes. We used two validation data sets derived from Complete Genomics (CG) sequencing: a set of publicly available genotypes on 69 samples (CG1), and a larger set of 250 individuals sequenced for the purposes of 1000GP validation (CG2). Both of these datasets contain accurate genotypes that were derived from high coverage (~80×), and show enough overlap in variants and samples with Phase 1 for relevant genotype discordance analysis. Supplementary Tables 2 and 3 show the overlap between the CG and 1000GP datasets in terms of samples and variant sites, respectively.
