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

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


We present an open-source algorithm, Scalpel (, 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • DNA / chemistry
  • DNA Mutational Analysis / methods*
  • Databases, Genetic
  • Exome*
  • Humans
  • INDEL Mutation*
  • Mutation
  • Programming Languages
  • Sequence Alignment
  • Software


  • DNA