Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

Variant callers for next-generation sequencing data: a comparison study.

PloS one - 1 Jan 2013

Liu Xiangtao, Han Shizhong, Wang Zuoheng, Gelernter Joel, Yang Bao-Zhu

Abstract excerpt

Next generation sequencing (NGS) has been leading the genetic study of human disease into an era of unprecedented productivity. Many bioinformatics pipelines have been developed to call variants from NGS data. The performance of these pipelines depends crucially on the variant caller used and on the calling strategies implemented. We studied the performance of four prevailing callers, SAMtools, GATK, glftools and...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Computational Biology
Share to Exome
Share to Genome, Human

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Genotype

Share to High-Throughput Nucleotide Sequencing

Share to Polymorphism, Single Nucleotide

Share to Sensitivity and Specificity

Share to Software

Source

Open in PubMed Open full text

Identifiers

PMID: 24086590
DOI: 10.1371/journal.pone.0075619
PMCID: PMC3785481

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 5 Sept 2026. Manifest publication-graph-cohort-2026-09-05.1.

Source receipt: pubmed, retrieved 5 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Variant callers for next-generation sequencing data: a comparison study.PMID 24086590Read ↗

Validation and assessment of variant calling pipelines for next-generation sequencing.Semantic proximity Read ↗

Comparison of variant callers using 60 532 multi-ancestry whole genome sequences.Semantic proximity Read ↗

Accuracy and efficiency of germline variant calling pipelines for human genome dataSemantic proximity Read ↗

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines.Semantic proximity Read ↗

Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discoverySemantic proximity Read ↗

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals.Semantic proximity Read ↗

Performance Assessment of Variant Calling Pipelines using Human Whole Exome Sequencing and Simulated dataSemantic proximity Read ↗

Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange.Semantic proximity Read ↗

Systematic comparison of variant calling pipelines using gold standard personal exome variants.Semantic proximity Read ↗

Discovering, Genotyping, and Annotating Structural Variants with the Genome Analysis Toolkit (GATK).Semantic proximity Read ↗

Best practices for variant calling in clinical sequencing.Semantic proximity Read ↗

Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.