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SPLINTER specifications


Unique identifier OMICS_00100
Alternative name Short indel Prediction by Large deviation Inference and Nonlinear True frequency Estimation by Recursion
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Aligned file and error model
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Diana Low
  • person_outline Robi Mitra
  • person_outline Todd Druley

Publications for Short indel Prediction by Large deviation Inference and Nonlinear True frequency Estimation by Recursion

SPLINTER citations


Pleiotropic Effects of Variants in Dementia Genes in Parkinson Disease

Front Neurosci
PMCID: 5902712
PMID: 29692703
DOI: 10.3389/fnins.2018.00230

[…] on an illumina genome analyzer iix (gaiix) according to the manufacturer's specifications. the resulting reads were re-aligned to the human genome reference assembly build 36.1 (hg18) using splinter. pcmv6-xl5 amplicon (1908 base pairs) was included in the reaction as a negative control. as positive controls, 10 different constructs (p53 gene) with synthetically engineered mutations […]


A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] such as mutect and vardict, accept single sample as input (). in addition, several algorithms are dedicated to perform single-sample variant calling. these algorithms include snvmix2, shearwater, splinter, snver, outlyzer, pisces, isown, somvarius, and sinvict , , , , , , , , and fall into two categories., snvmix2, shearwater, splinter, snver, outlyzer, and pisces report all variants without […]


Resequencing analysis of five Mendelian genes and the top genes from genome wide association studies in Parkinson’s Disease

Mol Neurodegener
PMCID: 4837564
PMID: 27094865
DOI: 10.1186/s13024-016-0097-0

[…] products. six dna samples heterozygous for previously known mutants in mapt gene were also included. single reads (36 bp) were aligned to the human genome reference assembly build 36.1 (hg18) using splinter []. splinter uses the positive control to estimate sensitivity and specificity for variant calling. the wild type: mutant ratio in the positive control is similar to the relative frequency […]


Sequencing of idiopathic pulmonary fibrosis related genes reveals independent single gene associations

PMCID: 4265083
PMID: 25553246
DOI: 10.1136/bmjresp-2014-000057

[…] illumina genome analyzer/miseq platform. negative and positive controls were inserted into the pooled sample to optimise detection of rare variants with high specificity and sensitivity. , we used splinter (short in/del prediction by large deviation inference and non-linear true frequency estimation by recursion) to identify rare single nucleotide variants and small insertions/deletions. […]


The PSEN1, p.E318G Variant Increases the Risk of Alzheimer's Disease in APOE ε4 Carriers

PLoS Genet
PMCID: 3750021
PMID: 23990795
DOI: 10.1371/journal.pgen.1003685

[…] the protein coding regions of the app, apoe, psen1, psen2, mapt and grn were obtained (table s2 in ). after adjusting for the sensitivity and specificity parameters of the base-calling algorithm (splinter) using negative and positive controls, a total of 396 and 369 variants were called and perfectly annotated in the targeted genomic regions of pool 1 and 2, respectively. 73% […]


Population based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

BMC Genomics
PMCID: 3534616
PMID: 23216810
DOI: 10.1186/1471-2164-13-683

[…] a single oligonucleotide regardless of index sequence. these results were obtained aligning raw reads against the entire genome using novoalign followed by variant calling of non-indexed pools using splinter or samtools for indexed samples. with these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. sensitivity, and to a lesser degree specificity, […]

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SPLINTER institution(s)
Center for Genome Sciences and Systems Biology Department of Genetics Washington University in St Louis School of Medicine, St Louis, MO, USA
SPLINTER funding source(s)
This work was partly supported by the Children's Discovery Institute grant MC-II-2006-1, the NIH Epigenetics Roadmap grant (1R01DA025744-01 and 3R01DA025744-02S1), the Saigh Foundation, and Hope Street Kids and Alex's Lemonade Stand “A” Award support.

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