Journal
NATURE METHODS
Volume 11, Issue 10, Pages 1033-1036Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.3069
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Funding
- US National Institutes of Health [R01-HG006677]
- US National Science Foundation [DBI-1350041]
- Cold Spring Harbor Laboratory (CSHL) Cancer Center Support Grant [5P30CA045508]
- Stanley Institute for Cognitive Genomics
- Simons Foundation [SF51, SF235988]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1350041] Funding Source: National Science Foundation
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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.
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