Skip to main content
Fig. 6 | BMC Medical Genomics

Fig. 6

From: AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting

Fig. 6

Overview of AMLVaran’s variant explorer. a Main view of the variant explorer. The detected variants are presented as a dynamic, customizable, interactive table that allows for comprehensive, easy-to-use real-time filtering. Variants can be filtered by gene name in the displayed gene panel, which shows all genes with their number of variants and allows the user to restrict the output to one or more genes. Further filtering options include the region type (exon, intron, hotspot regions), mutation type (non-synonymous, protein-coding, pathogenous effect prediction), and filtering by minimum quality values (coverage, variant allelic frequency, base quality). Certain kinds of variants can be excluded, e.g. variants rated as artifacts or polymorphisms by appreci8. The presented table can be easily adjusted by selecting the columns to be displayed, changing the sorting order and adding custom filters per column. b Detailed view of all annotation information available in AMLVaran for a variant. Information is divided into different tabs, which show the affected gene (name, function, pathways), the detected variant (protein effect, allele frequency, base quality), the effects of the variant in various medical databases, functional prediction scores from eight tools including rank scores with graphical representation, and a large number of literature references to the chosen gene and variant, retrieved on-the-fly from the constantly updated CiVIC database [49]

Back to article page