Variant Analysis Release Notes 2016


Release Spring

Software Version: 4.1.20160615

New Features

Ethnic group specific allele frequency information in Allele Frequency Community

In addition to variant composite frequency, users can now filter against East Asian, South Asian, African (American), European, and Hispanic sub-population frequencies in the Common Variants filter.

Compute allele frequencies from user-defined collection of samples

Empower users to establish their own “baseline” by computing frequencies based on a collection of samples (“My Libraries”), and annotating variants in a future analysis with library frequencies.

Make a copy of an existing analysis

Carry over analysis filter settings, samples, and sample metadata into a new analysis.


  • Added back the functionality to download original VCF
  • Added OMIM gene and phenotype ID to the variants table
  • Added GQ (Genotype Quality) to the Confidence Filter and VCF export
  • Revised compound het calculation to no longer include variants of uncertain significance
  • Retain allele depth (AD) information in exported VCF if uploaded VCF specifies the field
  • Improved handling of analyses where prefiltering produce zero variants
  • Increased numerical precision to 2 decimal points for variant call quality and allele fraction fields
  • Unified syntax for Allele Frequency Community fields across application UI and exported files (now reads as “AFC frequency” or “AFC_AF”)
  • API usage of Variant Analysis Custom Pipeline will now display the entire filter cascade, rather than only variants that survived the filter


Ingenuity Variant Analysis version 4.1.20160615
Content versions: CGI 54 Genomes (Version2.0), SIFT (2016-02-26), EVS (ESP6500SI-V2), Allele Frequency Community (2016-06-16), JASPAR (2013-11), Ingenuity Knowledge Base (Idris 160423.001), Vista Enhancer (2012-07), BSIFT (2016-02-26), TCGA (2013-09-05), PolyPhen-2 (v2.2.2), 1000 Genome Frequency (phase3v5b), Clinvar (2016-03-01), COSMIC (v76), ExAC (0.3), HGMD (2016.1), PhyloP (2019-11), DbSNP (146), TargetScan (6.2)


Release Winter 2015

GRCh38/hg20 genome build support. Given increasing traction in research and clinical community adoption of GRCh38, VCF files using GRCh38 coordinates can now be analyzed in Variant Analysis. Users can annotate, filter, and compare GRCh38 samples using updated versions of public databases (1000Genomes, dbSNP, ExAC, Exome Variant Server), as well as curated content.

 Filtering speed-up. Identified filtering bottlenecks and made optimizations to reduce time needed for compute/memory intensive tasks.