VarSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VarSeq
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Tool usage distribution map

This map represents all the scientific publications referring to VarSeq per scientific context
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Associated diseases

This word cloud represents VarSeq usage per disease context
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Protocols

VarSeq specifications

Information


Unique identifier OMICS_18804
Name VarSeq
Interface Web user interface
Restrictions to use License purchase required
Computer skills Basic
Stability Stable
Free trial Yes
Maintained Yes

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VarSeq citations

 (9)
call_split

Complex genetic architecture in severe hypobetalipoproteinemia

2018
PMCID: 5853080
PMID: 29540175
DOI: 10.1186/s12944-018-0680-1
call_split See protocol

[…] Targeted next-generation sequencing of genomic DNA comprised all known dyslipidemia genes, including MTTP (ABL gene), APOB (FHBL gene), PCSK9 and SAR1B (chylomicron retention disease gene) [, ]. VarSeq software prioritized possible or likely pathogenic rare variants of using the Online Mendelian Inheritance in Man database (https://www.ncbi.nlm.nih.gov/omim/). Prediction algorithms such as th […]

call_split

Identification of novel candidate genes for 46,XY disorders of sex development (DSD) using a C57BL/6J YPOS mouse model

2018
PMCID: 5789682
PMID: 29378665
DOI: 10.1186/s13293-018-0167-9
call_split See protocol

[…] s Unified Genotyper, then recalibrated and filtered using GATK variant-quality score recalibration and variant filtration tools. All high-quality variants were annotated using SNP&Variation Suite and VarSeq—variant filtration and annotation software (Golden Helix, USA). All variants were filtered by a minor allele frequency (MAF) of < 1% and intersected with the DSD gene list to identify mutations […]

library_books

Sequencing of Lynch syndrome tumors reveals the importance of epigenetic alterations

2017
Oncotarget
PMCID: 5746122
PMID: 29296220
DOI: 10.18632/oncotarget.22445

[…] In silico evaluation of somatic single nucleotide variants (SNVs) was conducted using VarSeq (GoldenHelix®) ( and ). VarSeq includes 6 individual algorithms to predict the effect of amino acid substitution on protein function: SIFT (http://sift.jcvi.org/), PolyPhen-2 [], MutationTaster […]

call_split

Identification of a novel mutation in the APTX gene associated with ataxia oculomotor apraxia

2017
PMCID: 5701303
PMID: 28652255
DOI: 10.1101/mcs.a002014
call_split See protocol

[…] ty scores, and cycle and context covariates. Variants were called with GATK HaplotypeCaller to generate genome variant call format (gVCF). Variant filtering and annotation was done using Golden Helix VarSeq Version 1.1 software (Golden Helix Inc.; http://goldenhelix.com/products/VarSeq/). The gVCF of each sequenced family member is uploaded to VarSeq and organized by pedigree. Variants are filtere […]

library_books

Use of next generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia[S]

2017
J Lipid Res
PMCID: 5665663
PMID: 28874442
DOI: 10.1194/jlr.D079301

[…] ol thresholds set for ratio and z-score metric outputs. Although proven robust in detection, our methodology has some limitations in further defining CNVs. In the event of a called “duplication,” the VarSeq CNV Caller output does not specify the exact degree of amplification. By design, this feature is a result of the difficulty in accurately differentiating DOC metrics as copy numbers incremental […]

call_split

Isolated Congenital Anosmia and CNGA2 Mutation

2017
Sci Rep
PMCID: 5454015
PMID: 28572688
DOI: 10.1038/s41598-017-02947-y
call_split See protocol

[…] ariant_index_parameter 128000. VQSR was used to recalibrate the variants, first with GATK VariantRecalibrator and then ApplyRecalibration. Variant filtering and annotation was done using Golden Helix VarSeq Version 1.1 software (http://goldenhelix.com/products/VarSeq/). After importing the variant call files (gVCF files) of each member of the family, the variants were organized by pedigree. Using […]


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VarSeq institution(s)
Golden Helix, Bozeman, MT, USA

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