Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-08

AUTHORS

Andy Rimmer, Hang Phan, Iain Mathieson, Zamin Iqbal, Stephen R F Twigg, WGS500 Consortium, Andrew O M Wilkie, Gil McVean, Gerton Lunter

ABSTRACT

High-throughput DNA sequencing technology has transformed genetic research and is starting to make an impact on clinical practice. However, analyzing high-throughput sequencing data remains challenging, particularly in clinical settings where accuracy and turnaround times are critical. We present a new approach to this problem, implemented in a software package called Platypus. Platypus achieves high sensitivity and specificity for SNPs, indels and complex polymorphisms by using local de novo assembly to generate candidate variants, followed by local realignment and probabilistic haplotype estimation. It is an order of magnitude faster than existing tools and generates calls from raw aligned read data without preprocessing. We demonstrate the performance of Platypus in clinically relevant experimental designs by comparing with SAMtools and GATK on whole-genome and exome-capture data, by identifying de novo variation in 15 parent-offspring trios with high sensitivity and specificity, and by estimating human leukocyte antigen genotypes directly from variant calls. More... »

PAGES

912-918

References to SciGraph publications

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ng.3036

    DOI

    http://dx.doi.org/10.1038/ng.3036

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1037327856

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25017105


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    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/ng.3036'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/ng.3036'

    RDF/XML is a standard XML format for linked data.

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