Scalpel is 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. It is based on the de Bruijn graph assembly paradigm and implements an on-the-fly repeat composition analysis coupled with a self-tuning k-mer strategy to increase specificity in regions characterized by complex repeat structures. It supports three different modes of operation:

  • Single: in single mode scalpel detects INDELs in one single dataset (e.g., one individual exome).
  • Denovo: in denovo mode scalpel detects de novo INDELs in one family of four individuals (mom, dad, aff, sib).
  • Somatic: in somatic mode scalpel detects somatic INDELs for a tumor/sample pair.

For all the modes of operation, scalpel requires that the raw reads have been previously aligned with BWA using default parameters. See BWA description for more info.

Scalpel is currently under active development and the user should expect to see changes in the output and command line parameters in the near future.

Obtaining Scalpel

Scalpel is hosted by The project page is here. Scalpel can be downloaded from the Sourceforge site at this address.