We introduce Giraffe, a pangenome short read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe, part of the variation graph toolkit (vg), maps reads to thousands of human genomes at around the same speed BWA-MEM maps reads to a single reference genome, while maintaining comparable accuracy to VG-MAP, vg's original mapper. We have developed efficient genotyping pipelines using Giraffe. We demonstrate improvements in genotyping for single

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... eotide variations (SNVs), insertions and deletions (indels) and structural variations (SVs) genome-wide. We use Giraffe to genotype and phase 167 thousands structural variations ascertained from long read studies in 5,202 human genomes sequenced with short reads, including the complete 1000 Genomes Project dataset, at an average cost of $1.50 per sample. We determine the frequency of these variations in diverse human populations, characterize their complex allelic variations and identify thousands of expression quantitative trait loci (eQTLs) driven by these variations.