ArrayStar provides a wide variety of tools for analyzing variants, including:

• Large-scale SNP comparisons across individuals and groups
• Advanced gene filtering based on the level of disruption to each gene caused by variations
• Comparison of groups of variants using text filters, tabular data, or graphical representations that include Venn diagrams, scatter plots and heat maps
• The ability to send genes or variants of interest to SeqMan Ultra to view the read alignment at that position; or to GenVision Pro to view the assembly coverage for all samples simultaneously

For human resequencing data, ArrayStar provides access to the Variant Annotation Database, which contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations include information about the frequency of the variant in the general population, in specific populations, and in publications, as well as information concerning the variant’s impact on functionality. The annotation information comes from several sources, including:

• Mastermind, the comprehensive database of genomic literature from Genomenon, providing access to NGS variant data from millions of PubMed publications.
• 1000 Genomes Project and the Exome Sequencing Project (ESP)
• dbNSFP v 4.1 which includes:

• Functional impact predictions from Sorting Intolerant from Tolerant (SIFT), MutationTaster, and the Likelihood Ratio Test (LRT).
• Evolutionary conservation scores from SiPhy, PhyloP, PhastCons and GERP++.
• Pathogenicity and clinical significance impact from ClinVar.
• Basic amino acid sequence information, Database of Single Nucleotide Polymorphism (dbSNP) IDs, and annotations from Uniprot and Interpro.