title: 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.
authors.affiliation: 1] Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] New York Genome Center, New York, USA.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Narzisi
authors.affiliation: 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.
authors.forename: Jason A
authors.initials: JA
authors.lastname: O'Rawe
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Iossifov
authors.affiliation: 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.
authors.forename: Han
authors.initials: H
authors.lastname: Fang
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Yoon-Ha
authors.initials: YH
authors.lastname: Lee
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Zihua
authors.initials: Z
authors.lastname: Wang
authors.affiliation: 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.
authors.forename: Yiyang
authors.initials: Y
authors.lastname: Wu
authors.affiliation: 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.
authors.forename: Gholson J
authors.initials: GJ
authors.lastname: Lyon
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Wigler
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D004252:DNA Mutational Analysis / Q000379:methods*; D030541:Databases, Genetic; D059472:Exome; D006801:Humans; D054643:INDEL Mutation; D009154:Mutation; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software
chemical_list: D004247:DNA