A reference panel of 64,976 haplotypes for genotype imputation
Shane McCarthy, Sayantan Das, Warren Kretzschmar, Richard Durbin, Goncalo Abecasis, Jonathan Marchini
bioRxiv doi: http://dx.doi.org/10.1101/035170
We describe a reference panel of 64,976 haplotypes at 39,235,157 SNPs constructed using whole genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1%, a large increase in the number of SNPs tested in association studies and can help to refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.