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Reference-based phasing using the Haplotype Reference Consortium panel
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DOI：10.1038/ng.3679.png)
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Abstract
En 中文
Haplotype phasing is a fundamental problem in medical and population genetics. Phasing is generally performed via statistical phasing in a genotyped cohort, an approach that can yield high accuracy in very large cohorts but attains lower accuracy in smaller cohorts. Here we instead explore the paradigm of reference-based phasing. We introduce a new phasing algorithm, Eagle2, that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the Haplotype Reference Consortium; HRC) using a new data structure based on the positional Burrows-Wheeler transform. We demonstrate that Eagle2 attains a similar to 20x speedup and similar to 10% increase in accuracy compared to reference-based phasing using SHAPEIT2. On European ancestry samples, Eagle2 with the HRC panel achieves >2x the accuracy of 1000 Genomes-based phasing. Eagle2 is open source and freely available for HRC-based phasing via the Sanger Imputation Service and the Michigan Imputation Server.
Keywords:
GENETIC EPIDEMIOLOGY RESEARCH
GENOTYPE IMPUTATION
LINKAGE DISEQUILIBRIUM
ADULT HEALTH
INFERENCE
RECONSTRUCTION
ASSOCIATION
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