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Protocols

SNPTools specifications

Information


Unique identifier OMICS_00075
Name SNPTools
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License BSD 2-clause “Simplified” License, MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Fuli Yu
  • person_outline James Lu

Additional information


https://sourceforge.net/p/snptools/wiki/Home/

Publication for SNPTools

SNPTools citations

 (15)
library_books

A missense mutation in TCN2 is associated with decreased risk for congenital heart defects and may increase cellular uptake of vitamin B12 via Megalin

2017
Oncotarget
PMCID: 5589654
PMID: 28903415
DOI: 10.18632/oncotarget.19377

[…] al libraries were equivalently pooled and then hybridized to RNA library baits. Sequencing was performed on an Illumina HiSeq2000 DNA sequencer (version 3, Illumina, Inc.). Variants were called using SNPTools [], and the variants with a quality score below 1.5 were eliminated. Variants were annotated with gene function data from UCSC and known variants were assigned respective SNP codes as dbSNP13 […]

library_books

Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice

2017
Genetics
PMCID: 5499176
PMID: 28592500
DOI: 10.1534/genetics.116.198051

[…] genes in the interacting regions using biomaRt (, ). We identified which of these genes had SNPs corresponding to their haplotype effects by querying the Sanger SNP database (; ) using the R package SNPTools (). We further filtered the genes based on functional annotation. We focused on motifs influencing the immune module and thus filtered the genes in each region to those annotated to the Mouse […]

library_books

Extremely low coverage whole genome sequencing in South Asians captures population genomics information

2017
BMC Genomics
PMCID: 5440948
PMID: 28532386
DOI: 10.1186/s12864-017-3767-6

[…] l file : Section S2)). The coverages in the simulated dataset closely matched that of the SAS-AP dataset (Additional file : Section S2). When the variance ratio statistic parameter (s) is set at 2.8, SNPTools [] recovered all single nucleotide variants (SNVs) with minor allele frequency (MAF) ≥ 10%. The false discovery rate was bounded by 3%, where the majority of false positive sites had a MAF <  […]

library_books

11,670 whole genome sequences representative of the Han Chinese population from the CONVERGE project

2017
Sci Data
PMCID: 5308202
PMID: 28195579
DOI: 10.1038/sdata.2017.11

[…] fter optimizing for Transition to Transversion (TiTv) ratios in SNPs called. Genotype likelihoods (GLs) were calculated at selected sites using a sample-specific binomial mixture model implemented in SNPtools (version 1.0), and imputation was performed at those sites without a reference panel using BEAGLE (version 3.3.2). A second round of imputation was performed with BEAGLE on the same GLs, but […]

call_split

Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model

2016
Sci Rep
PMCID: 5095882
PMID: 27811965
DOI: 10.1038/srep36123
call_split See protocol

[…] ive allele SNPs. In order to further assure high quality and statistically robust SNP identification in an initial small discovery cohort of 8 animals, three tools were used to call SNPs (Atlas-SNP2, SNPTools, and ssahaSNP) and the only SNPs called by all three tools were selected as candidates for further analysis. Variant Effect Predictor (VEP) based on rhesus gene models was used to identify fu […]

library_books

SNP based heritability estimates of the personality dimensions and polygenic prediction of both neuroticism and major depression: findings from CONVERGE

2016
PMCID: 5290344
PMID: 27779626
DOI: 10.1038/tp.2016.177

[…] n. A sensitivity threshold of 90% was applied for imputation after optimizing for Transition to Transversion ratios. Genotype likelihoods were calculated using a binomial mixture model implemented in SNPtools (version 1.0) and imputation was performed at sites with no reference panel using BEAGLE (version 3.3.2). A second round of imputation was performed at biallelic polymorphic SNPs using 1000 G […]


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SNPTools institution(s)
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, Institution of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Department of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA; Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
SNPTools funding source(s)
Supported by the NIH-NHGRI grants 5U01HG005211 and 2U54HG003273.

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