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Nat Methods. 2014 Oct;11(10):1033-6. doi: 10.1038/nmeth.3069. Epub 2014 Aug 17.

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

Author information

1
1] Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] New York Genome Center, New York, USA.
2
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.
3
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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.

PMID:
25128977
PMCID:
PMC4180789
DOI:
10.1038/nmeth.3069
[Indexed for MEDLINE]
Free PMC Article

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