ShapeIt2 phased haplotypes for the Phase1 integrated variant calls

2013-09-17 00:00:00 +0100

Olivier Delaneau and Jonathan Marchini have provided improved haplotypes for the phase1 integrated call set on the autosomes generated using SHAPEIT2.

Using a set of validation genotypes at SNP and biallelic indels Olivier and Jonathan have been able to show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low frequency.