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NGS-SNP specifications


Unique identifier OMICS_00177
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens




No version available


  • person_outline Paul Stothard

Publication for NGS-SNP

NGS-SNP citations


Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole genome sequence variants

PMCID: 5889553
PMID: 29625549
DOI: 10.1186/s12711-018-0387-9

[…] ed for the four traits (2025 for each trait, with 245 shared between at least two traits).The imputed whole-genome variants were annotated based on the Sscrofa 10.2 assembly of the swine genome using NGS-SNP []. All variants were then defined as belonging to one of three broad categories, as suggested by MacLeod et al. []. The first category, which will be referred to as “NSC”, comprised variants […]


Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

BMC Genomics
PMCID: 5885354
PMID: 29618315
DOI: 10.1186/s12864-018-4617-x

[…] are available on request.All dairy phenotypic records (including both cow and bull records) were published and available from the study by Kemper et al. [].All SNP annotations were obtained from the NGS-SNP pipeline [] and annotations can be obtained from the authors from that study. […]


Multi breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect

PMCID: 5609075
PMID: 28934948
DOI: 10.1186/s12711-017-0347-9

[…] vided into four groups based on their functional annotations: NSC variants, REG variants, variants on the HD chip and all other variants. Annotations for the sequence variants were collated using the NGS-SNP software []. LD pruning was first performed within each group, followed by removal of REG variants with an r2 higher than 0.9 with a NSC variant, HD variants with an r2 higher than 0.9 with a […]


Novel gene function revealed by mouse mutagenesis screens for models of age related disease

Nat Commun
PMCID: 4992138
PMID: 27534441
DOI: 10.1038/ncomms12444
call_split See protocol

[…] ary of SNVs. The overlapping sites were removed resulting in a final list of unique ENU SNVs for each G1. These SNVs were then functionally annotated (for example, missense, intronic and so on) using NGS-SNP. All high-confidence mutations are available on MouseBook. For individual mutant lines SNVs were confirmed by Sanger sequencing of affected mice. […]


Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9 mediated homology directed repair

Genome Med
PMCID: 4753642
PMID: 26876963
DOI: 10.1186/s13073-016-0273-4
call_split See protocol

[…] and single nucleotide variants (SNVs) were called by GATK’s UnifiedGenotyper, both using dbSNP version 137 as the background single nucleotide polymorphism (SNP) set. SNV annotations were done using NGS-SNP []. Indels were annotated using The Variant Effect Predictor [].SNVs and indels were then compared against the precompiled list found in 18 inbred strains from the Mouse Genome Project []. Fur […]


Rare Variants in Transcript and Potential Regulatory Regions Explain a Small Percentage of the Missing Heritability of Complex Traits in Cattle

PLoS One
PMCID: 4671594
PMID: 26642058
DOI: 10.1371/journal.pone.0143945

[…] lculated as the proportion of non-matching homozygotes between parent-offspring pairs and collected per pair and per locus. SNPs and indels were annotated with predicted functional consequences using NGS-SNP [], []. The sequenced variants that were identified during annotation were restricted to the coding regions and potentially regulatory regions (including 3’ and 5’ untranslated gene regions an […]


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NGS-SNP institution(s)
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
NGS-SNP funding source(s)
Supported by Alberta Livestock and Meat Agency and the Natural Sciences and Engineering Research Council of Canada.

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