SNPTools protocols

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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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Documentation


Maintainers


  • person_outline Fuli Yu <>
  • person_outline James Lu <>

Additional information


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

Publication for SNPTools

SNPTools in pipelines

 (2)
2016
PMCID: 5018196
PMID: 27612449
DOI: 10.1186/s12859-016-1211-6

[…] have higher sensitivity compared to consensus 3of4 approach but the smallest fdr value (gotcloud) among the callers is ~6 % which is almost twice that of the consensus 3of4 approach (see table ). snptools has lower sensitivity than consensus 3of4 but recovers most common variants (1000g, dbsnp) compared to the other callers at only 10 % of the computation resource cost. using some combination […]

2014
PMCID: 4338501
PMID: 25653097
DOI: 10.1038/ncomms4934

[…] genotype gl: p (r|gl), where gl = 0, 1, 2 counts the number of non-reference alleles in the genotype. these genotype likelihoods can be obtained using specialised software like samtools [], snptools [] or gatk [] that derive these likelihoods directly from the bam files containing the sequence reads., in each iteration we must sample a pair of haplotypes (h1, h2) for the ith individuals […]


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SNPTools in publications

 (8)
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 &l […]

PMCID: 5308202
PMID: 28195579
DOI: 10.1038/sdata.2017.11

[…] 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, […]

PMCID: 5095882
PMID: 27811965
DOI: 10.1038/srep36123

[…] relaxed to allow for 3 of 4 and 2 of 4 in one cohort, but still absent in the comparison cohort ()., to assure high quality snp identification, we used three tools to call snps (atlas-snp2, snptools, and ssahasnp) and only selected the 1534 snps called by all three for further analysis ( and ). the snps were initially called using ssahasnp […]

PMCID: 5018196
PMID: 27612449
DOI: 10.1186/s12859-016-1211-6

[…] wgs freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. the callers used were snptools, gatk-haplotypecaller, gatk-unifiedgenotyper and gotcloud. we used amazon aws, a 4000-core in-house cluster at baylor college of medicine, ibm power pc blue biou at rice and rhea at oak […]

PMCID: 4522619
PMID: 26176920
DOI: 10.1038/nature14659

[…] 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, […]


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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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