Identify causal variants from human sequencing data in just minutes

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Ingenuity Variant Analysis is a HIPAA-compliant, web-based application that helps researchers studying disease to identify causal variants from human sequencing data in just hours. Variant Analysis combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and your own knowledge of disease biology. With Variant Analysis, you can interrogate your variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow-up.  Only Variant Analysis offers an interactive filter cascade that uses a single source of accurate, curated content − the Ingenuity® Knowledge Base.  Supported workflows include:

Stratification Studies
Large Cancer Studies
Genetic Disease Cohorts
Trio/Quad Studies
Tumor-Normal Pairs
Personal Genomes


What file formats can I use to upload my data?
Answer:  Variant Analysis currently supports Variant Call Format (VCF), Genome Variation Format (GVF), and Complete Genomics’ files (MasterVar, High confidence junction, etc.).  Please see our article about file format ( ) for more details.

How do I interpret my data?
 Ingenuity Variant Analysis™ will merge the variants from all the variant files you selected into a single analysis, and annotate all the variants using the latest available content from the Ingenuity Knowledge Base. Please see our article about exploring your data ( ) for a general information  about exploring the result and/or the Filters and Analytics Overview section for specific information.

How are genes defined in Variant Analysis?
Answer: NCBI Reference Sequences (RefSeqs, see are used to define genes since they are curated evidence-based RNA sequences. Ingenuity Variant Analysis maps the current RefSeq sequences for each gene (a gene can have multiple transcripts, which are RNA isoforms resulting from alternative splicing) onto the human reference genome to identify the location(s) where there is at least a complete 5’ sequence, if not full-length, match. Flanking promoter and introns between exons corresponding to regions matching the RefSeq RNA sequence are added to define the gene model, the contiguous DNA sequence span containing the gene (collection of mapped transcripts). The gene model defines the non-overlapping gene regions that distinguish promoter, untranslated, coding, splice sites, etc. within this span for each transcript.

Can I integrate RNA-Seq data or expression data with my DNA re-sequencing data?
Answer: Yes.  You can use the Custom Annotation Filter to create filters based on RNA-Seq/expression data that you import into Variant Analysis.  Please see our custom annotation filter articles ( ) for more details.

I see a filter cascade, can I customize it?
Answer: Yes you can move and edit any filters, so the result are tailor to your specific workflow. You can also add new filtering option.  Please see our article about exploring your data ( ) for a general information and/or the Filters and Analytics Overview section for specific information.

Where can I find versioning information for the data sources used?
Answer: You can find a comprehensive listing of both public data sources and Ingenuity Knowledge Base, along with versions used, at​.

I need help, do you offer scientific and technical support, trainings, workflows, etc?
Answer:  Yes, we offer a variety of resource from hot line suport to recorded and free web training. Please see our Training and Seminar article ( ) for more details about our trainings and workflows. You can also contact our support desk where we have PhD level scientists are available to answer your scientific and technical questions at:

Where can I find more information on Variant Analysis' hosted infrastructure security, HIPPA and Safe Harbor compliance, and data privacy?
Answer: You can find more information regarding our privacy policy here:
Additional information regarding our hosted infrastructure security, HIPPA and Safe Harbor compliance, and data privacy can be found in the white paper here: 
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