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SNPTools specifications


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




No version available



  • person_outline Fuli Yu
  • person_outline James Lu

Additional information

Publication for SNPTools

SNPTools citations


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

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 […]


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

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 […]


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

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

[…] iation, coverage as low as 0.1x may be sufficient to infer fine-scaled ancestry information among worldwide continental populations []. Indeed, with multiple sample joint-calling and genotyping using SNPTools, followed by SNPTools imputation, we achieved excellent calling accuracy for heterozygous SNVs (Additional file : Section S4.2). Even for sites that have no coverage in an individual, we achi […]


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

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 […]


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

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 […]


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

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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