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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Vydané v:	Bioinformatics (Oxford, England) Ročník 28; číslo 5; s. 724 - 725
Hlavní autori:	Makarov, Vladimir, O'Grady, Tina, Cai, Guiqing, Lihm, Jayon, Buxbaum, Joseph D., Yoon, Seungtai
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Oxford Oxford University Press 01.03.2012
Predmet:	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
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Abstract	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.
AbstractList	UNLABELLED: 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. 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. http://anntools.sourceforge.net/. Supplementary data are available at Bioinformatics online. 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.UNLABELLEDAnnTools 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.http://anntools.sourceforge.net/.AVAILABILITYhttp://anntools.sourceforge.net/.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. 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. 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.
Author	Makarov, Vladimir Buxbaum, Joseph D. Cai, Guiqing O'Grady, Tina Yoon, Seungtai Lihm, Jayon
AuthorAffiliation	1 The Seaver Autism Center for Research and Treatment, 2 Department of Psychiatry, 3 Levy Library, Mount Sinai School of Medicine, New York, NY 10029, USA, 4 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA, 5 Department of Neuroscience, 6 Department of Genetics and Genomic Sciences and 7 The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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SubjectTerms	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
Title	AnnTools: a comprehensive and versatile annotation toolkit for genomic variants
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