Alamut Batch


Alamut® Batch is a high-throughput annotation software for NGS analysis.

alamut suite process annotation

Designed for intensive variant analysis workflows (gene panels or exomes), Alamut® Batch enriches raw NGS variants with dozens of attributes including effects on human genes, detailed information on known variants and mutations, predictions on the pathogenic status of missense variations as well as splicing predictions.

Gifted with numerous features, Alamut® Batch is available in a client/server version (available on Linux and Windows) or in a standalone version (available on Linux). The Windows client/server version offers a graphical user interface. The standalone version is faster but needs to be installed in-house by the user.

Both versions of Alamut® Batch can be easily integrated into existing NGS analysis pipelines.

Rated as one of the most comprehensive variant annotation tools, Alamut® Batch is powerful, efficient and benefits from a fast and easy installation process. Developed for clinical diagnostic and research laboratories, Alamut Batch enriches raw variants with a wealth of reliable and regularly updated attributes. They include effects on human genes characterized on RefSeq transcripts or LRG sequences, accurate HGVS nomenclature descriptions, allele frequencies from different public databases such as 1000Genomes and ExAC, annotations with phenotypes from ClinVAR, COSMIC and HGMD Pro and on biological processes with Gene Ontology annotations. Alamut Batch computes predictions to assess the functional consequences of missense variants thanks to SIFT and Align GVGD. Alamut Batch also provides advanced splicing effect predictions based on MaxEntScan, SSF and other splicing prediction tools.

Alamut® Batch takes as input a list of genomic variations and outputs a list of annotations for each variant located inside a human gene locus. VCF files and tab-delimited files are supported for variant input.

The output file with annotated variants is a tab-delimited file with variants in rows and annotations in columns. This format is identical whatever Alamut Batch version is used.

The annotated variants can be easily filtered with Alamut Focus, the interactive variant filtration application.

Alamut Batch complies with the ACMG/AMP Variant Interpretation Standards and Guidelines. Click here for details.

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What they say
about Alamut Visual

"I recommend Alamut to all of my colleagues and friends in genomics!"

Duke University, Durham, USA



ESHG 2017



ACMG 2017