Genomic sequencing-based variants calls for GM12878 were generated by the Broad Institute. Illumina Human-1MDuo BeadChip array genotype data generated by the HusdonAlpha Institute of Biotechnology for GM12878 and 52 other ENCODE samples were obtained from the UCSC genome browser [26 ]. Autosomal genotypes for all 53 samples were imputed using MaCH-Admix [27 (link)] with default parameter settings and the reference panel from the 1000 Genomes Project Phase I version 3 (2012-03-14 release). Chromosome X genotype data in the 53 samples were pre-phased using MaCH [28 (link)] with options --states 500 and --rounds 400 and then imputed using minimac [29 (link)] with options --state 10 and --rounds 10. Post-imputation filtering of variants according to Rsq was performed as previously reported [30 (link)].
Common alleles (MAF > 0.05) used to derive the initial custom reference genome were based on 1000 Genomes Phase I version 3 EUR population [31 ].
Common alleles (MAF > 0.05) used to derive the initial custom reference genome were based on 1000 Genomes Phase I version 3 EUR population [31 ].
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