Indel variant analysis of short-read sequencing data with Scalpel

Fang, H., Bergmann, E. A., Arora, K., Vacic, V., Zody, M. C., Iossifov, I., O'Rawe, J. A., Wu, Y., Jimenez Barron, L. T., Rosenbaum, J., Ronemus, M., Lee, Y. H., Wang, Z., Dikoglu, E., Jobanputra, V., Lyon, G. J., Wigler, M., Schatz, M. C., Narzisi, G. (2016) Indel variant analysis of short-read sequencing data with Scalpel. Nat Protoc, 11 (12). pp. 2529-2548. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

URL: https://www.ncbi.nlm.nih.gov/pubmed/27854363
DOI: 10.1038/nprot.2016.150

Abstract

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 (http://scalpel.sourceforge.net) 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 approximately 5 h after read mapping.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > insertion/deletion
Investigative techniques and equipment > assays > next generation sequencing
CSHL Authors:
Communities: CSHL labs > Iossifov lab
CSHL labs > Lyon lab
CSHL labs > Schatz lab
CSHL labs > Wigler lab
Depositing User: Matt Covey
Date Deposited: 29 Nov 2016 20:57
Last Modified: 16 Jun 2017 16:45
Related URLs:
URI: http://repository.cshl.edu/id/eprint/33902

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