AnnTools protocols

View AnnTools computational protocol

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AnnTools specifications


Unique identifier OMICS_00166
Name AnnTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Variant calls
Output format VCF
Operating system Unix/Linux, Mac OS
Programming languages Python
Database management system MySQL
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes


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  • person_outline Vladimir Makarov <>

Publication for AnnTools

AnnTools in pipeline

PMCID: 5540655
PMID: 28808687
DOI: 10.1212/NXG.0000000000000177

[…] insertions/deletions (indels) were called using the gatk unified genotyper tool, where calls were filtered based on mapping quality (q30 or higher) and depth of coverage (d10 or higher). last, the anntools kit was used for annotation of the resulting calls, and picard was used to conduct exomes' statistics (, genomic variations observed as common mutations (frequency […]

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AnnTools in publications

PMCID: 4827795
PMID: 27081306
DOI: 10.4137/CIN.S30793

[…] cancerous genes. its potential has been waiting to be explored. these databases provide different types of valuable genetic information, made easily accessible by software tools such as snpeff, anntools, annovar (, and oncotator ( more recently, another database-based method, […]

PMCID: 4868688
PMID: 26673618
DOI: 10.18632/oncotarget.6543

[…] molecule”, “neuropeptide”, “neurotransmitter”, “neurotrophic factor”, and “neurotrophic molecule” to consult those databases., after using “2one” software tool ( to detect and delete genes repeated in the results of the three searches, we had a final list of 2688 genes., we used transgp software […]

PMCID: 4618522
PMID: 26490036
DOI: 10.1186/s12864-015-1991-5

[…] to generate subpopulation-level cnvrs. details of merging criteria and breakpoint assignment are found in additional file : supplementary methods., subpopulation-specific cnvrs were annotated using anntools (version 1.1), in which the following genomic features were annotated against genome build 37 (hg19): cytobands, genes (and affected exons), micrornas, transcription factor binding sites […]

PMCID: 4216909
PMID: 25339461
DOI: 10.1186/1756-0500-7-747

[…] sample calling., figure 1 figure 2 , for all three evaluation data sets, although illumina supplied annotated vcf files, we annotated both illumina and gatk vcf files using snpeff [] and anntools [] to provide a uniform annotation for comparison between pipelines., the summarized comparison results between the casava and gatk pipeline are presented in table  . both casava and gatk […]

PMCID: 4179605
PMID: 25288875
DOI: 10.4137/CIN.S13789

[…] from the ucsc table browser or through the mysql site ( there are many tools designed to annotate, visualize, or manipulate vcf files such as vcftools, annovar, and anntools. other programs, such as haploreg, can take lists of snp identifiers to annotate variants with regulatory annotations in the attempt to streamline bioinformatics follow-up of gwas loci. […]

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AnnTools institution(s)
The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York, NY, USA; Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA; Levy Library, Mount Sinai School of Medicine, New York, NY, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Department of Neuroscience, Mount Sinai School of Medicine, New York, NY, USA; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA; The Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY, USA
AnnTools funding source(s)
Supported by the Seaver Foundation; Simons Foundation and NIMH (grants MH089025 and MH093725).

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