ngsLD: evaluating linkage disequilibrium using genotype likelihoods

TY - JOUR

T1 - ngsLD

T2 - evaluating linkage disequilibrium using genotype likelihoods

AU - Fox, Emma A.

AU - Wright, Alison E.

AU - Fumagalli, Matteo

AU - Vieira, Filipe G.

PY - 2019/10/1

Y1 - 2019/10/1

N2 - MOTIVATION: Linkage disequilibrium (LD) measures the correlation between genetic loci and is highly informative for association mapping and population genetics. As many studies rely on called genotypes for estimating LD, their results can be affected by data uncertainty, especially when employing a low read depth sequencing strategy. Furthermore, there is a manifest lack of tools for the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with limited sample sizes. RESULTS: ngsLD addresses these issues by estimating LD directly from genotype likelihoods in a fast, reliable and user-friendly implementation. This method makes use of the full information available from sequencing data and provides accurate estimates of linkage disequilibrium patterns compared with approaches based on genotype calling. We conducted a case study to investigate how LD decays over physical distance in two avian species. AVAILABILITY AND IMPLEMENTATION: The methods presented in this work were implemented in C/C and are freely available for non-commercial use from https://github.com/fgvieira/ngsLD. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - MOTIVATION: Linkage disequilibrium (LD) measures the correlation between genetic loci and is highly informative for association mapping and population genetics. As many studies rely on called genotypes for estimating LD, their results can be affected by data uncertainty, especially when employing a low read depth sequencing strategy. Furthermore, there is a manifest lack of tools for the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with limited sample sizes. RESULTS: ngsLD addresses these issues by estimating LD directly from genotype likelihoods in a fast, reliable and user-friendly implementation. This method makes use of the full information available from sequencing data and provides accurate estimates of linkage disequilibrium patterns compared with approaches based on genotype calling. We conducted a case study to investigate how LD decays over physical distance in two avian species. AVAILABILITY AND IMPLEMENTATION: The methods presented in this work were implemented in C/C and are freely available for non-commercial use from https://github.com/fgvieira/ngsLD. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

UR - http://www.scopus.com/inward/record.url?scp=85071975264&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btz200

DO - 10.1093/bioinformatics/btz200

M3 - Journal article

C2 - 30903149

AN - SCOPUS:85071975264

SN - 1367-4811

VL - 35

SP - 3855

EP - 3856

JO - Bioinformatics (Online)

JF - Bioinformatics (Online)

IS - 19

ER -