Chunk #46 — Methods — Haplotype estimation

Source: The UK Biobank resource with deep phenotyping and genomic data.
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Haplotype estimation (phasing) was carried out using SHAPEIT3 in chunks of 15,000 markers, with an overlap of 250 markers between chunks. Each chunk used 4 cores per job and S = 200 copying states. Chunks were ligated using a modified version of the hapfuse program (https://bitbucket.org/wkretzsch/hapfuse/src).