Alamut Batch

Features of Alamut® Batch

Alamut Batch offers numerous features and dozens of annotations for the NGS analysis of your variants


Alamut Batch is an efficient high-throughput human variant annotation engine for large studies like NGS analysis.
The annotation engine supports human genes (protein coding, non-protein coding and pseudogenes).
The data enrichment is based on the well-curated Alamut® software Suite database and on efficient external prediction tools.
Alamut Batch is easy to integrate into any analysis pipeline (Linux, Windows).
It uses standard bioinformatics file formats (e.g. tab-delimited, VCF).


The annotations can be restricted/limited to user-defined regions. The external annotations supplied in variant annotation files can be integrated in the output.
A GUI frontend is available on Windows.
Alamut Batch is available as a client-server or standalone application (including the Alamut® database).


Variant location, type, coding effects, HGVS nomenclature

  • Gene: symbol, HGNC id, OMIM® id
  • Transcripts: RefSeq id, strand, length
  • Protein: RefSeq id, Uniprot id, domains
  • Variant type: substitution, deletion, insertion, duplication, delins
  • Coding effect: synonymous, missense, nonsense, in-frame, frameshift, start loss, stop loss
  • Variant location: upstream, 5’UTR, exon, intron, 3’UTR, downstream
  • gDNA-level, cDNA-level, protein-level HGVS nomenclature
  • Exon and/or intron number

Identification with variation databases

  • dbSNP, ExAC, ESP/EVS
  • ClinVar, SwissProt
  • COSMIC (available at no extra cost to both academic and commercial users — users who wish to download the COSMIC database, manipulate or mine it directly would need to obtain it from the Sanger Institute)

Splicing predictions

  • MaxEntScan, NNSPLICE, SpliceSiteFinder, GeneSplicer predictions
  • Effect on nearest natural splice site
  • Splicing effect in variation vicinity (e.g. new splice site, activation of nearby cryptic site)
  • Branch point predictions

Missense annotations and predictions

  • phastCons and phyloP nucleotide conservation scores
  • Codon detailed annotations
  • Amino acid conservation in orthologues
  • BLOSUM scores, Grantham distance, amino acid physico-chemical features
  • Growing list of missense prediction tools: SIFT, Align GVGD, MAPP

What they say
about Alamut

"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 2019



ESHG 2019