SVS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SVS

Tool usage distribution map

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

This word cloud represents SVS usage per disease context

Popular tool citations

chevron_left Variant effect prediction CNV detection Normalization Genotype imputation Differential expression chevron_right
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SVS specifications


Unique identifier OMICS_02051
Name SVS
Alternative name SNP & Variation Suite
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Golden Helix GenomeBrowse

SVS citations


Canine leishmaniasis: Genome wide analysis and antibody response to Lutzomyia longipalpis saliva

PLoS One
PMCID: 5942812
PMID: 29742167
DOI: 10.1371/journal.pone.0197215
call_split See protocol

[…] f the fitted models were used as pseudo-phenotypes to test the association between genotypes and phenotypes in a mixed linear model controlled for polygenic effects and sample structure (EMMAX) [] in SNP & Variation Suite (SVS) v.8 (Golden Helix, Inc., Bozeman, MT, USA, Genotypes were filtered in order to remove SNPs with a call rate below 95%, a minor allele frequency (MAF) […]


Genome wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

BMC Genomics
PMCID: 5930521
PMID: 29716533
DOI: 10.1186/s12864-018-4699-5

[…] ce for SNP-based GWAS studies, including studies of large populations of livestock. As a result, software packages have been developed and published for CNV prediction from SNP chip data, such as the SNP & Variation Suite (SVS; Golden Helix, Bozeman, MT), which facilitate a low-cost approach to detect common CNV within a population for GWAS analysis [, ].Because Holsteins are the largest milk-prod […]


PITX2 deficiency and associated human disease: insights from the zebrafish model

Hum Mol Genet
PMCID: 5932568
PMID: 29506241
DOI: 10.1093/hmg/ddy074

[…] et of interest were calculated, and the Z-score for each replicate was derived by dividing the difference between the replicate and the mean by the standard deviation. Z-scores were imported into the SNP and Variation Suite software (Golden Helix, Inc., Bozeman, MT) for heatmap synthesis. […]


Genetic variation in Aquaporin 4 moderates the relationship between sleep and brain Aβ amyloid burden

PMCID: 5865132
PMID: 29479071
DOI: 10.1038/s41398-018-0094-x
call_split See protocol

[…] ver2.3, with the 1000 genome reference panel (2015 release). SNP data from the AQP4 genomic region (GRCh37 Chr18:24,432,000–24,446,000) were extracted and subjected to quality control in GoldenHelix SNP and Variation Suite (SVS version 8.7.1), which included removal of SNPs with call rate < 95%, Minor allele frequency < 5% and departure from Hardy–Weinberg Equilibrium (p < 0.05), leaving 32 SNPs […]


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

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

[…] rvals ± 2 bp using GATK’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 li […]


Genome wide association study in Asia adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance

Sci Rep
PMCID: 5762920
PMID: 29321632
DOI: 10.1038/s41598-017-18690-3

[…] The PCA method described by Price et al. was implemented in the SNP & Variation Suite (SVS) V_8.6.0 (SVS, Golden Helix, Inc., Bozeman, MT, www. A three-dimensional plot of the first three principal components was drawn to visualize the possible p […]

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

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