Format

Send to

Choose Destination
Database (Oxford). 2014 Oct 3;2014. pii: bau098. doi: 10.1093/database/bau098. Print 2014.

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.

Author information

1
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden adam.ameur@igp.uu.se.
2
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.

Abstract

CanvasDB is an infrastructure for management and analysis of genetic variants from massively parallel sequencing (MPS) projects. The system stores SNP and indel calls in a local database, designed to handle very large datasets, to allow for rapid analysis using simple commands in R. Functional annotations are included in the system, making it suitable for direct identification of disease-causing mutations in human exome- (WES) or whole-genome sequencing (WGS) projects. The system has a built-in filtering function implemented to simultaneously take into account variant calls from all individual samples. This enables advanced comparative analysis of variant distribution between groups of samples, including detection of candidate causative mutations within family structures and genome-wide association by sequencing. In most cases, these analyses are executed within just a matter of seconds, even when there are several hundreds of samples and millions of variants in the database. We demonstrate the scalability of canvasDB by importing the individual variant calls from all 1092 individuals present in the 1000 Genomes Project into the system, over 4.4 billion SNPs and indels in total. Our results show that canvasDB makes it possible to perform advanced analyses of large-scale WGS projects on a local server. Database URL: https://github.com/UppsalaGenomeCenter/CanvasDB.

PMID:
25281234
PMCID:
PMC4184106
DOI:
10.1093/database/bau098
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center