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Related Experiment Video

Updated: Oct 17, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing.

H Busra Cagirici1, Bala Ani Akpinar2, Taner Z Sen1

  • 1Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, CA 94710, USA.

International Journal of Molecular Sciences
|October 13, 2021
PubMed
Summary

Variant calling in hexaploid wheat (Triticum aestivum) requires careful tool selection and filtering. This study assessed whole exome sequencing pipelines, finding that filtering improves accuracy and reproducibility for genetic variation analysis.

Keywords:
BCFtoolsBWABowtie2SNPsSTARWESvariantswheat

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • The hexaploid wheat genome (Triticum aestivum) is complex, yet advancements in reference genomes facilitate understanding trait variation.
  • Variant calling in polyploids like wheat presents challenges in tool selection and false-positive filtering compared to diploids.

Purpose of the Study:

  • To evaluate the performance of different variant calling pipelines using whole exome sequencing (WES) data in 48 wheat cultivars.
  • To determine the impact of various computational methods on variant identification accuracy and reproducibility in polyploid wheat.

Main Methods:

  • Whole exome sequencing (WES) was performed on 48 diverse wheat cultivars.
  • Multiple variant calling pipelines were assessed using their default settings for read alignment and variant identification.
  • Performance metrics including sensitivity and precision were analyzed for raw and filtered SNP calls.

Main Results:

  • All assessed variant calling pipelines necessitated post-calling filtering to remove false positives.
  • The best-performing pipelines demonstrated high consensus in called SNPs after filtering, indicating reliable results.
  • Detailed comparisons revealed varying levels of sensitivity and precision across pipelines for both raw and filtered data.

Conclusions:

  • Filtering is essential for accurate and reproducible variant calling in hexaploid wheat whole exome sequencing data.
  • The study provides a comparative analysis to guide the selection of optimal variant calling strategies for polyploid wheat genomics.
  • Understanding pipeline performance is crucial for leveraging genomic variation in wheat breeding and research.