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A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). Scalpel is designed to perform localized micro-assembly of specific regions of interest with the goal of detecting mutations with high accuracy and increased power. Scalpel supports three modes of operation: single, de novo, and somatic. In the single mode, Scalpel detects indels in one single dataset (e.g., one individual exome). In the de novo mode, Scalpel detects de novo indels in a quad family (father, mother, affected child, unaffected sibling). In the somatic mode, Scalpel detects somatic indels from the sequencing data coming from matched tumor and normal samples.

Software type:
Command line interface
Restrictions to use:
Operating system:
Programming languages:
C++, Perl
Computer skills:
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  • Giuseppe Narzisi <gnarzisi at nygenome.org>


Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, NY, USA, 11724; New York Genome Center, New York, USA

  • (Fang et al., 2015) Indel variant analysis of short-read sequencing data with Scalpel. bioRxiv.
    DOI: 10.1101/028050
  • (Narzisi et al., 2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature methods.
    PMID: 25128977
  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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