Alamut Batch


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

Designed for intensive variant analysis workflows (gene panels or exomes), Alamut® Batch enriches raw NGS variants with dozens of attributes from private or public databases 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.

Considered by our customers as being 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 external 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 provides in silico 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

"We are very grateful for the work you do with Alamut and continuing to improve it. We use it on daily basis to help us interpret variants for clinical tests including our technicians, analysts, genetic counselors and lab directors. Alamut has the comprehensive information available for interpreting variants and great documentation. I’ve recommended Alamut to many customers who ask me about the tools that I use. Many thanks to you for making this possible."

Cincinnati Children's Hospital Medical Center



ASHG 2018



ESHG 2018