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Updated: Jun 25, 2026
05:30
Indel Detection following CRISPR/Cas9 Mutagenesis using High-resolution Melt Analysis in the Mosquito Aedes aegypti
Published on: September 10, 2021
Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes
Biorxiv : the Preprint Server for Biology
|June 24, 2026
Summary
Complex indels, often from DNA double-strand breaks (DSB), are challenging to analyze. FreeBayes most accurately represented these complex variants, enabling better analysis of DNA repair events.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Complex indels involve both deletions and insertions, often near boundaries.
- These variants frequently result from double-strand breaks (DSB) repaired by nonhomologous DNA end joining (NHEJ).
- Existing indel callers struggle with complex indel representation in VCF files.
Purpose of the Study:
- To evaluate the performance of different variant calling approaches in representing complex indels.
- To develop a workflow for analyzing complex indels derived from DSB repair.
Main Methods:
- Tested six variant calling pipelines: FreeBayes, HaplotypeCaller, Mutect2, Strelka2, DRAGEN Germline, and DRAGEN Somatic.
- Simulated complex indels to assess variant representation.
- Developed a parsing workflow for FreeBayes VCF output.
Main Results:
- FreeBayes demonstrated the most consistent representation of simulated complex indels as single variant records.
- The developed parsing workflow effectively derives deleted and inserted sequences.
- The approach aids in analyzing DSB repair events in human colon crypts.
Conclusions:
- FreeBayes offers superior representation of complex indels compared to other tested callers.
- A novel parsing workflow enhances the analysis of complex indels.
- This methodology facilitates the study of endogenous DSB repair mechanisms.
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