Ingenuity Variant Analysis protocols

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Ingenuity Variant Analysis statistics

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Ingenuity Variant Analysis specifications

Information


Unique identifier OMICS_05452
Name Ingenuity Variant Analysis
Interface Web user interface
Restrictions to use License purchase required
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Ingenuity Variant Analysis Team <>

Additional information


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Ingenuity Variant Analysis in pipelines

 (14)
2018
PMCID: 5839370
PMID: 29515789
DOI: 10.18632/oncotarget.24273

[…] that are homozygous. if the mutation occurs with a mutation percentage ≤ 80%, the mutation is excluded if the ratio of forward and reverse reads is < 0.1. variants were then annotated using ingenuity variant analysis (iva, 2017 winter release) software (qiagen, redwood city, ca). variants referenced in iva proprietary knowledge base with an allele frequency ≥ 1% in the general […]

2018
PMCID: 5850229
PMID: 29431102
DOI: 10.1161/JAHA.117.006428

[…] across all 4 samples simultaneously using the genome analysis toolkit's unifiedgenotyper with variant quality score recalibration. the resultant variant call format files were analyzed with qiagen's ingenuity variant analysis software using an iterative filtering process. to determine rarity of variants, minor allele frequencies from 3 publicly available databases were utilized: 1000 genomes […]

2017
PMCID: 5440144
PMID: 28514307
DOI: 10.1097/MD.0000000000006914

[…] time analysis. the reads were mapped to the reference human genome (human 37.3; snp135) using nextgene software (softgenetics llc, state college, pa). wes generated a total of 34,350 variants. the ingenuity variant analysis (ingenuity systems, mountain view, ca) was used to analyze the candidate variants. the following variants were initially excluded: the common variants with the minor allele […]

2017
PMCID: 5477361
PMID: 28327575
DOI: 10.1038/ejhg.2017.32

[…] data from three families where bam files were available in ega were re-analysed with an analysis pipeline that combined multi-sample variant calling with platypus and variant prioritisation using ingenuity variant analysis (www.ingenuity.com/products/variant-analysis), similar to that described previously. for three families where bam files were not available in ega at the time […]

2017
PMCID: 5655919
PMID: 28748566
DOI: 10.1111/bjh.14863

[…] calling was performed by a maximum likelihood approach on a bayesian model. variants were called with a minimum of 9 ×  coverage, 3 counts and 25% frequency. variants were further filtered using the ingenuity variant analysis tool (qiagen), excluding the low quality scores and variants (>1% in background population), and including variants found within the 87‐gene list and variants associated […]


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Ingenuity Variant Analysis in publications

 (70)
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] in supplementary table ., joint variant calling was performed with gatk’s haplotypecaller. this included de novo assembly at each potential variant locus. variants were annotated and analysed using ingenuity variant analysis (iva) software (qiagen, redwood city, ca, usa), mutationtaster2, snpeff, seattleseq annotation server, and galaxy (via usegalaxy.org). allele frequencies and additional […]

PMCID: 5933810
PMID: 29684080
DOI: 10.1371/journal.pgen.1007352

[…] analysis toolkit (gatk, ) []. we implemented the exome hidden markov model (xhmm) algorithm to call copy number variations (cnvs) from wes (, )., wes variants were annotated and classified using ingenuity variant analysis (iva, qiagen, redwood city, california), which classifies variants according to acmg guidelines [, ] (). we prioritized variants with a minor allele frequency (maf) ≤0.01 […]

PMCID: 5920151
PMID: 29732366
DOI: 10.3389/fped.2018.00114

[…] clinical research exome kit. paired-end sequencing was performed on illumina instruments, with an average coverage of 50–100×. data were processed using qiagen's biomedical genomics workbench and ingenuity variant analysis. rna sequencing was performed using illumina's truseq stranded total rna library prep kit and paired-end sequencing was performed to gain an average output of 50–100 m […]

PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] were annotated using variantstudio v2 (illumina), a software using variant effect predictor (vep) v2.8, cosmic v77 and 1000 genomes (v3). in a second approach, data were analyzed using qiagen's ingenuity variant analysis software (qiagen redwood city)., for copy-number and zygosity detection and analyses, log2r values were generated from paired and unpaired tumor and germline data […]

PMCID: 5902396
PMID: 29368431
DOI: 10.1002/mgg3.357

[…] and wgs was performed as described (khromykh et al., ). filtering for candidate pathogenic variants was conducted with an internally developed analysis pipeline and two commercial pipelines, ingenuity variant analysis (qiagen inc., valencia, ca, usa), and personalis research analysis service (personalis, inc., menlo park, ca, usa), both applied by the vendors. for the internal pipeline, […]


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