LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data
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LocalNgsRelate : a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. / Severson, Alissa L.; Korneliussen, Thorfinn Sand; Moltke, Ida.
In: Bioinformatics, Vol. 38, No. 4, 2022, p. 1159-1161.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - LocalNgsRelate
T2 - a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data
AU - Severson, Alissa L.
AU - Korneliussen, Thorfinn Sand
AU - Moltke, Ida
PY - 2022
Y1 - 2022
N2 - Motivation: Inference of identity-by-descent (IBD) sharing along the genome between pairs of individuals has important uses. But all existing inference methods are based on genotypes, which is not ideal for low-depth Next Generation Sequencing (NGS) data from which genotypes can only be called with high uncertainty.Results: We present a new probabilistic software tool, LocalNgsRelate, for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. Its inference is based on genotype likelihoods instead of genotypes, and thereby it takes the uncertainty of the genotype calling into account. Using real data from the 1000 Genomes project, we show that LocalNgsRelate provides more accurate IBD inference for low-depth NGS data than two state-of-the-art genotype-based methods, Albrechtsen et al. (2009) and hap-IBD. We also show that the method works well for NGS data down to a depth of 2x.
AB - Motivation: Inference of identity-by-descent (IBD) sharing along the genome between pairs of individuals has important uses. But all existing inference methods are based on genotypes, which is not ideal for low-depth Next Generation Sequencing (NGS) data from which genotypes can only be called with high uncertainty.Results: We present a new probabilistic software tool, LocalNgsRelate, for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. Its inference is based on genotype likelihoods instead of genotypes, and thereby it takes the uncertainty of the genotype calling into account. Using real data from the 1000 Genomes project, we show that LocalNgsRelate provides more accurate IBD inference for low-depth NGS data than two state-of-the-art genotype-based methods, Albrechtsen et al. (2009) and hap-IBD. We also show that the method works well for NGS data down to a depth of 2x.
KW - IDENTITY-BY-DESCENT
U2 - 10.1093/bioinformatics/btab732
DO - 10.1093/bioinformatics/btab732
M3 - Journal article
C2 - 34718411
VL - 38
SP - 1159
EP - 1161
JO - Bioinformatics (Online)
JF - Bioinformatics (Online)
SN - 1367-4811
IS - 4
ER -
ID: 298035138