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Short-read aligner performance in germline variant identification

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: I...

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Detalles Bibliográficos
Autores principales: Wilton, Richard, Szalay, Alexander S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10421969/
https://www.ncbi.nlm.nih.gov/pubmed/37527006
http://dx.doi.org/10.1093/bioinformatics/btad480
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author Wilton, Richard
Szalay, Alexander S
author_facet Wilton, Richard
Szalay, Alexander S
author_sort Wilton, Richard
collection PubMed
description 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.
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spelling pubmed-104219692023-08-13 Short-read aligner performance in germline variant identification Wilton, Richard Szalay, Alexander S Bioinformatics Review 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. Oxford University Press 2023-08-01 /pmc/articles/PMC10421969/ /pubmed/37527006 http://dx.doi.org/10.1093/bioinformatics/btad480 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Wilton, Richard
Szalay, Alexander S
Short-read aligner performance in germline variant identification
title Short-read aligner performance in germline variant identification
title_full Short-read aligner performance in germline variant identification
title_fullStr Short-read aligner performance in germline variant identification
title_full_unstemmed Short-read aligner performance in germline variant identification
title_short Short-read aligner performance in germline variant identification
title_sort short-read aligner performance in germline variant identification
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10421969/
https://www.ncbi.nlm.nih.gov/pubmed/37527006
http://dx.doi.org/10.1093/bioinformatics/btad480
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