Short-read aligner performance in germline variant identification

Author:

Wilton Richard1ORCID,Szalay Alexander S12

Affiliation:

1. Department of Physics and Astronomy, Johns Hopkins University , Baltimore, MD 21218, United States

2. Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, United States

Abstract

Abstract Motivation Read alignment is an essential first step in the characterization of DNA sequence variation. The accuracy of variant-calling results depends not only on the quality of read alignment and variant-calling software but also on the interaction between these complex software tools. Results In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant-calling accuracy. We examine the performance of three general-purpose short-read aligners—BWA-MEM, Bowtie 2, and Arioc—in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant-calling performance.

Funder

National Institutes of Health

National Cancer Institute

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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