Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

18.8K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
18.8K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.9K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.9K
Multiple Allele Traits01:49

Multiple Allele Traits

38.4K
The Concept of Multiple Allelism
38.4K
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

59
The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
59
Genetic Variation01:25

Genetic Variation

1.5K
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
1.5K
Human Genetics01:28

Human Genetics

1.7K
Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
1.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Indirect genomic effects shape cancer risk across species.

bioRxiv : the preprint server for biology·2026
Same author

The Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026
Same author

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Nature methods·2026
Same author

A complete human pancreatic cancer genome.

bioRxiv : the preprint server for biology·2026
Same author

The Common Fund Data Ecosystem (CFDE).

bioRxiv : the preprint server for biology·2026
Same author

Learning Explainable Imaging-Genetics Associations Related to a Neurological Disorder.

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention·2026

Related Experiment Video

Updated: Feb 28, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.6K

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.

Ruibang Luo1,2, Michael C Schatz1,2, Steven L Salzberg1,2,3

  • 1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.

Gigascience
|June 23, 2017
PubMed
Summary

16GT is a new variant caller that unifies single nucleotide polymorphism and insertion/deletion detection for whole-genome sequencing. It shows improved SNP sensitivity and comparable indel accuracy against established tools.

Keywords:
Bayesian modelSNP callingindel callingvariant calling

More Related Videos

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

10.8K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K

Related Experiment Videos

Last Updated: Feb 28, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.6K
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

10.8K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.0K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate variant calling is crucial for genomic research and clinical applications.
  • Existing variant callers often handle single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) separately.
  • There is a need for unified and efficient algorithms for variant detection.

Purpose of the Study:

  • To introduce 16GT, a novel variant caller designed for Illumina sequencing data.
  • To present a unified probabilistic model for simultaneous SNP and indel calling.
  • To evaluate the performance of 16GT against other leading variant callers.

Main Methods:

  • Development of a 16-genotype probabilistic model for variant calling.
  • Integration of SNP and indel calling into a single algorithm.
  • Benchmarking 16GT against five other variant callers using whole-genome and whole-exome sequencing data.

Main Results:

  • 16GT demonstrated superior sensitivity in calling single nucleotide polymorphisms.
  • 16GT achieved comparable sensitivity and accuracy for insertion and deletion calling relative to GATK HaplotypeCaller.
  • Performance was evaluated on a modern multi-core server.

Conclusions:

  • 16GT offers an effective unified approach for variant calling from Illumina sequencing data.
  • The tool provides competitive performance, particularly in SNP detection.
  • 16GT is available as open-source software for the research community.