AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants ar...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 28; no. 5; pp. 724 - 725
Main Authors: Makarov, Vladimir, O'Grady, Tina, Cai, Guiqing, Lihm, Jayon, Buxbaum, Joseph D., Yoon, Seungtai
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 01.03.2012
Subjects:
Applications Note
Biological and medical sciences
DNA Copy Number Variations
Fundamental and applied biological sciences. Psychology
General aspects
Genetic Variation
Genome, Human
Human health sciences
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Molecular Sequence Annotation
Polymorphism, Single Nucleotide
Sciences de la santé humaine
Software
Genomics
Annotation
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
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Description
Summary:AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps with regulatory elements, disease/trait associated loci, known segmental duplications and artifact prone regions, thereby offering an integrated and comprehensive analysis of genomic data. The tool conveniently accepts user-provided tracks for custom annotation and offers flexibility in input data formats. The output is generated in the universal Variant Call Format. High annotation speed makes AnnTools suitable for high-throughput sequencing facilities, while a low-memory footprint and modest CPU requirements allow it to operate on a personal computer. The application is freely available for public use; the package includes installation scripts and a set of helper tools. Availability:  http://anntools.sourceforge.net/ Contact:  vladimir.makarov@mssm.edu; chris.yoon@mssm.edu Supplementary information:  Supplementary data are available at Bioinformatics online.
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scopus-id:2-s2.0-84857831329
Associate Editor: Martin Bishop
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/bts032