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VariantStudio specifications

Information


Unique identifier OMICS_07006
Name VariantStudio
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

VariantStudio citations

 (22)
call_split

Next generation sequencing reveals a new mutation in the LTBP2 gene associated with microspherophakia in a Spanish family

2018
BMC Med Genet
PMCID: 5948732
PMID: 29751740
DOI: 10.1186/s12881-018-0590-0
call_split See protocol

[…] 1, LTBP2, ADAMTS10, ADAMTS17) in the clinical exome panel. Amplified samples following the TSO protocol were loaded onto the MIseq instrument according to the manufacturer’s instructions (Illumina©). VariantStudio software® (Illumina©) allowed us to analyze the files from the experiment. Sanger sequencing was used to validate the NGS results.To investigate whether IBD (identity by descent) occurs […]

call_split

Compound heterozygous TYK2 mutations underlie primary immunodeficiency with T cell lymphopenia

2018
Sci Rep
PMCID: 5934390
PMID: 29725107
DOI: 10.1038/s41598-018-25260-8
call_split See protocol

[…] program (http://bio-bwa.sourceforge.net). Genetic variants were identified with the Genome Analysis Toolkit (https://software.broadinstitute.org/gatk/), followed by data annotation using the Illumina VariantStudio software. Analyses of the SVs from the exome sequencing data were performed using the programs, Pindel, Delly and gridss (https://github.com/PapenfussLab/gridss), at their default settin […]

call_split

Discovery of genetic variants of the kinases that activate tenofovir among individuals in the USA, Thailand, and South Africa: HPTN067

2018
PLoS One
PMCID: 5895070
PMID: 29641561
DOI: 10.1371/journal.pone.0195764
call_split See protocol

[…] ic, New York, NY). Fifty ng of DNA input were used per DNA sample sequenced. The resulting prepared DNA library (6 μL) was diluted in 594 μL HT1 buffer containing 1% PhiX sequencing control. Illumina VariantStudio software was used to annotate and analyze variant read quality as previously described []. To predict the consequences of the detected variants on kinase activity the in silico tools SIF […]

library_books

Clinically actionable mutation profiles in patients with cancer identified by whole genome sequencing

2018
PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] single nucleotide (SNV) and insertion/deletion (InDel) variant calling analysis was performed using the Tumour-Normal Application v1.0, based on Strelka, within BaseSpace. Calls 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 […]

library_books

Comprehensive molecular biomarker identification in breast cancer brain metastases

2017
J Transl Med
PMCID: 5747948
PMID: 29287594
DOI: 10.1186/s12967-017-1370-x

[…] d by the corresponding BED file []. The generated VCF files were uploaded to the Illumina BaseSpace Hub and variants were annotated and classified according to their biological significance using the VariantStudio App 1.0.0. Major filter settings included read depth > 10, no reported global and population frequencies (de facto = 0), and variant calling of mutations, comprising frameshift, stop gai […]

call_split

Next Generation Sequencing identifies mutations in GNPTG gene as a cause of familial form of scleroderma like disease

2017
PMCID: 5615433
PMID: 28950892
DOI: 10.1186/s12969-017-0200-2
call_split See protocol

[…] ome assembly 19 (UCSC hg19)) recommended by GATK best practices: mapping was performed using BWA-MEM, variant calling using GATK (haplotypecaller). Annotation and filtering steps were performed using VariantStudio (Illumina). We first removed non exonic variants and variants indicated as synonymous, Variants files of parents and index case were confronted: only variants that fulfilled recessive in […]

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VariantStudio institution(s)
Illumina, San Diego, CA, USA

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