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Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.

Indel variant analysis of short-read sequencing data with Scalpel.

Author information

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Stony Brook University, Stony Brook, New York, USA.
New York Genome Center, New York, New York, USA.
Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.
Columbia University Medical Center, New York, New York, USA.
Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.


As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel ( is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation: single-sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ∼5 h after read mapping.

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