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Related Experiment Video

Updated: Jul 5, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Short-read aligner performance in germline variant identification.

Richard Wilton¹, Alexander S Szalay^1,2

¹Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, United States.

Bioinformatics (Oxford, England)

|August 1, 2023

Summary

Optimizing DNA sequence variant calling requires careful selection of short-read aligners and variant callers. This study evaluates BWA-MEM, Bowtie 2, and Arioc with DeepVariant, FreeBayes, and GATK HaplotypeCaller to improve germline variant-calling accuracy.

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Last Updated: Jul 5, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

Targeted DNA Methylation Analysis by Next-generation Sequencing

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Published on: February 24, 2015

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate DNA sequence variation characterization relies on precise read alignment.
Variant-calling accuracy is influenced by aligner quality, caller software, and their interactions.

Conclusions:

The choice of read aligner and variant caller, along with their configurations, is crucial for accurate germline variant calling.
Understanding these interactions can guide the optimization of variant-calling pipelines.
Further research into software tool interactions is warranted for advancing genomic analysis.