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. 2013 Feb 1;41(3):e46.
doi: 10.1093/nar/gks1143. Epub 2012 Dec 5.

A population model for genotyping indels from next-generation sequence data

Haojing Shao  1 , Evangelos Bellos, Hanjiudai Yin, Xiao Liu, Jing Zou, Yingrui Li, Jun Wang, Lachlan J M Coin
Affiliations

A population model for genotyping indels from next-generation sequence data

Haojing Shao et al. Nucleic Acids Res. .

Abstract

Insertion and deletion polymorphisms (indels) are an important source of genomic variation in plant and animal genomes, but accurate genotyping from low-coverage and exome next-generation sequence data remains challenging. We introduce an efficient population clustering algorithm for diploids and polyploids which was tested on a dataset of 2000 exomes. Compared with existing methods, we report a 4-fold reduction in overall indel genotype error rates with a 9-fold reduction in low coverage regions.

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Figures

Figure 1.
Figure 1.
Illustration of population clustering method on real data. (A–D) Clustering at different putative indel sites, with different depth of coverage, as well as site-specific error rates. Each point represents the total number of aligned reads (X-axis), as well as the number of indel aligned reads (Y-axis) for each individual in the population. Shapes indicate the genotype called by SOAP-popIndel: squares, circles and triangles indicate homozygous reference, heterozygous and homozygous indels, respectively. (A and C) low-to-medium depth of coverage, low error rate. Panel B: medium-to-high depth of coverage, low error rate. (D) low-to-medium depth of coverage, high error rate.
Figure 2.
Figure 2.
Genotyping accuracy and missing rates. Dashed-line, solid line, circles and diamonds represent SOAP-popIndel, Dindel, SAMTools and piCALL, respectively. Black: real exome data; Red: 4× simulation; Green: 20× simulation and Blue: 40× simulation. Lines for Dindel and SOAP-popIndel are based on posterior probability thresholds between 0.90 and 0.99. SAMTools and piCALL do not report probability of assignment, so are represented by a single point. (A) Results on 44 Sequenom validated sites. (B) Restricted to sites within samples that had <5× coverage. (C) Results on simulated data.
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