SVS protocols

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SVS specifications

Information


Unique identifier OMICS_19321
Name SVS
Alternative name SNP and Variation Suite
Software type Application/Script
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

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Additional information


http://goldenhelix.com/products/SNP_Variation/index.html

SVS in pipelines

 (6)
2017
PMCID: 5651560
PMID: 29085643
DOI: 10.1186/s40575-017-0052-6

[…] another round of annotation was carried out to remove variants not called in all 8 samples, creating a second vcf file. a commercially available sequence annotation software package (golden helix snp and variation suite, golden helix inc., bozeman, mt) was used to differentiate between the ls negative and ls positive dogs. two separate selection settings were used to identify variants […]

2017
PMCID: 5702371
PMID: 28866788
DOI: 10.1007/s00439-017-1838-z

[…] hard filtering instead of variant quality score recalibration was applied to variants (mckenna et al. ). a vcf file containing variants was downloaded from the yale computing cluster and read with snp and variation suite version 8 (golden helix, inc., bozeman, mt). variants altering protein sequence (counts are reported in table ) were filtered for only those with minor allele frequencies […]

2015
PMCID: 4315167
PMID: 25923178
DOI: 10.1186/1471-2164-16-S1-S8

[…] was performed using default settings of the lifescope software (life technologies, carlsbad, ca). high quality variants (with coverage >=10x and mqv>=20) were annotated and filtered using the snp and variation suite (svs) version 7 from golden helix. novel and rare variants (with maf <1%) were filtered against the nhlbi exome project database. snvs were predicted damaging using […]

2014
PMCID: 4053598
PMID: 24509779
DOI: 10.1007/s00439-014-1427-3

[…] had an overall call rate <85 %, were not used for genetic analyses. in the discovery alspac cohort, single marker snp analyses of case–control status and quantitative traits were completed using snp and variation suite (svs) v7.6.4 (bozeman, mt). linkage disequilibrium was assessed and haplotype blocks were constructed using the four-gamete rule option in haploview v4.2. haplotype-based […]

2013
PMCID: 3591355
PMID: 23505534
DOI: 10.1371/journal.pone.0058552

[…] component analysis (pca), a widely used method for identifying and visualizing patterns of population structure . it was carried out using the genotypic principal components analysis module of snp and variation suite v.7.4.0. to obtain non-overestimated eigenvectors , we first ran the software using an outlier removal procedure, in which individuals with values that were greater than six […]


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SVS in publications

 (64)
PMCID: 5951800
PMID: 29760470
DOI: 10.1038/s41598-018-25801-1

[…] genotyping quality. all study samples (both discovery and validation data) had a cqc values >2., principle component analysis was performed using eigenstrat algorithm implemented in golden helix snp and variation suite v8.5.0. genotype data from 270 hapmap samples were used as reference to infer genetic ancestry of the study samples. variance was accounted for by the top two principal […]

PMCID: 5864572
DOI: 10.5770/cgj.21.320

[…] (mmse) and montreal cognitive assessment (moca) were used. genomic dna was extracted from white blood cells and genotyped using illumina 2.5. the chromosome 21 cnv analysis was performed using snp and variation suite (svs). statistical analysis was performed using chi-squared test and mann whitney u test., this preliminary cnv analysis of chromosome 21 did not show significant association […]

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

[…] 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), […]

PMCID: 5795417
PMID: 29295533
DOI: 10.3390/v10010004

[…] in genetics, clinical medicine, and bioinformatics within the past few years []. in this study, we used the recursive partitioning methods based interactive tree analysis tool in helixtree snp and variation suite version 6.4.3 (golden helix, inc., bozeman, mt, usa) to analyze the large pool of sequence variants of the three important sites (pbs, sd, and ps) within the 5′ltr leader […]

PMCID: 5744078
PMID: 29312441
DOI: 10.3389/fgene.2017.00218

[…] estimates, 497,294 snps were subjected to linkage disequilibrium (ld) pruning using the parameter (50 5 0.20), yielding 80,602 snps., genotypic data for the 600k and 50k platforms were merged using snp and variation suite v.8.5.0 (golden helix, bozeman, mt, united states ). a total of 41,752 snps overlapping between the two platforms were filtered according to quality control criteria; snps […]


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