Paragraph: a graph-based structural variant genotyper for short-read sequence data.
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ABSTRACT:
SUBMITTER: Chen S
PROVIDER: S-EPMC6921448 | biostudies-literature | 2019 Dec
REPOSITORIES: biostudies-literature
Publications
Paragraph: a graph-based structural variant genotyper for short-read sequence data.
Chen Sai S Krusche Peter P Dolzhenko Egor E Sherman Rachel M RM Petrovski Roman R Schlesinger Felix F Kirsche Melanie M Bentley David R DR Schatz Michael C MC Sedlazeck Fritz J FJ Eberle Michael A MA
Genome biology 20191219 1
Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long-read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples ...[more]
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