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Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings.

ABSTRACT: Comprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min ratio: 1.3~3.4). The similarity between variant call sets was more closely determined by VCAs rather than by short-read aligners. Remarkably, reported minor allele frequency had a substantial effect on concordance between pipelines (concordance rate ratio: 0.11~0.92; Wald tests, P?

SUBMITTER: Hwang KB 

PROVIDER: S-EPMC6397176 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings.

Hwang Kyu-Baek KB   Lee In-Hee IH   Li Honglan H   Won Dhong-Geon DG   Hernandez-Ferrer Carles C   Negron Jose Alberto JA   Kong Sek Won SW  

Scientific reports 20190301 1

Comprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min r  ...[more]

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