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Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

ABSTRACT: We present an open-source algorithm, Scalpel (http://scalpel.sourceforge.net/), which combines mapping and assembly for sensitive and specific discovery of insertions and deletions (indels) in exome-capture data. A detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for indel discovery, particularly in regions containing near-perfect repeats. We analyzed 593 families from the Simons Simplex Collection and demonstrated Scalpel's power to detect long (?30 bp) transmitted events and enrichment for de novo likely gene-disrupting indels in autistic children.

SUBMITTER: Narzisi G

PROVIDER: S-EPMC4180789 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

Narzisi Giuseppe G O'Rawe Jason A JA Iossifov Ivan I Fang Han H Lee Yoon-Ha YH Wang Zihua Z Wu Yiyang Y Lyon Gholson J GJ Wigler Michael M Schatz Michael C MC

Nature methods 20140817 10

We present an open-source algorithm, Scalpel (http://scalpel.sourceforge.net/), which combines mapping and assembly for sensitive and specific discovery of insertions and deletions (indels) in exome-capture data. A detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for indel discovery, particularly in regions containing near-perfect repeats. We analyzed 593 families from the Simons Simplex Collection and demonstrated ...[more]

PMID: 25128977

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