Alamut® Focus allows the user to quickly design and apply simple to complex variant filtering strategies with an intuitive and easy-to-use graphical user interface.
It also allows to apply pre-configured inheritance-based scenarios: autosomal recessive, autosomal dominant, X-linked recessive, de novo.
It is fully compatible with ALAMUT® BATCH and ALAMUT® VISUAL.
Variant location, type, frequency, genotype, coding effects, biological processes, and molecular functions
- Gene: symbol and location within a gene
- Variant type: substitution, deletion, insertion, duplications, delins
- Genotype : homozygote, heterozygote and variant frequency
- Coding effect: synonymous, missense, nonsense, in-frame, frameshift, start loss, stop loss
- Variant location: upstream, downstream, exon, intron, 5’UTR, 3’UTR, splice site
- Gene Ontology terms (biological process, cellular component, molecular function)
- Allele frequency
Information and allele frequencies from variation databases
- dbSNP, ExAC, ESP/EVS, 1000 Genomes
Missense annotations and predictions, splicing predictions
- Growing list of missense prediction tools: SIFT, Align GVGD, MAPP
- Splicing effect in variation vicinity (e.g. new splice site, activation of nearby cryptic site)
- Variant calling quality: Phred quality score, filter status
- Mapping quality
- Depth of coverage
- autosomal recessive or dominant,
- X-linked recessive,
- de novo mutation
Starting from annotated variant collections, the software selects candidate variations based on user-defined or pre-configured criteria.