A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.
Am J Hum Genet
; 106(4): 426-437, 2020 04 02.
Article
en En
| MEDLINE
| ID: mdl-32169169
ABSTRACT
Segments of identity by descent (IBD) are used in many genetic analyses. We present a method for detecting identical-by-descent haplotype segments in phased genotype data. Our method, called hap-IBD, combines a compressed representation of haplotype data, the positional Burrows-Wheeler transform, and multi-threaded execution to produce very fast analysis times. An attractive feature of hap-IBD is its simplicity the input parameters clearly and precisely define the IBD segments that are reported, so that program correctness can be confirmed by users. We evaluate hap-IBD and four state-of-the-art IBD segment detection methods (GERMLINE, iLASH, RaPID, and TRUFFLE) using UK Biobank chromosome 20 data and simulated sequence data. We show that hap-IBD detects IBD segments faster and more accurately than competing methods, and that hap-IBD is the only method that can rapidly and accurately detect short 2-4 centiMorgan (cM) IBD segments in the full UK Biobank data. Analysis of 485,346 UK Biobank samples through the use of hap-IBD with 12 computational threads detects 231.5 billion autosomal IBD segments with length ≥2 cM in 24.4 h.
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Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Genoma Humano
/
Análisis de Secuencia de ADN
Límite:
Humans
Idioma:
En
Revista:
Am J Hum Genet
Año:
2020
Tipo del documento:
Article
País de afiliación:
Estados Unidos