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 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.
Alamut Batch integrates annotations from HGMD® Professional* (BIOBASE).
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)
  • HGMD® Professional (requires separate subscription from QIAGEN)

Splicing predictions

  • MaxEntScan, NNSPLICE, Human Splicing Finder, 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 Visual

"We were early Alamut adopters and this software has become essential to our daily diagnosis lab practice, saving time and reducing mistakes. The intuitivity of use and the new functionalities are a very useful help in our daily work."

Paris, France



ESHG 2017



ACMG 2017