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Protocols

SVS specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Golden Helix GenomeBrowse

SVS citations

 (117)
call_split

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

2018
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, www.goldenhelix.com). Genotypes were filtered in order to remove SNPs with a call rate below 95%, a minor allele frequency (MAF) […]

library_books

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

2018
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 […]

library_books

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

2018
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. […]

call_split

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

2018
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 […]

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

[…] 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 […]

library_books

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

2018
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. goldenhelix.com). A three-dimensional plot of the first three principal components was drawn to visualize the possible p […]

Citations

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

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