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IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing.

Matthew Jobin1,2, Haiko Schurz3, Brenna M Henn4

  • 1Department of Anthropology, Santa Clara University.

Genome Biology and Evolution
|May 4, 2018
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Summary

IMPUTOR software accurately imputes missing genomic data and corrects sequencing errors in nonrecombining haploid genomes. This phylogenetically aware tool achieves high accuracy for genomic variant imputation and error correction.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing generates large genomic datasets, often with missing or erroneous data due to low coverage.
  • Accurate imputation and error correction are crucial for downstream genomic analyses, especially for nonrecombining regions like the Y-chromosome.

Purpose of the Study:

  • To introduce IMPUTOR, a novel software tool for phylogenetically aware imputation of missing haploid nonrecombining genomic data.
  • To evaluate IMPUTOR's accuracy in imputing missing genotypes and correcting sequencing errors.

Main Methods:

  • IMPUTOR utilizes the principle of parsimony for data imputation.
  • The software is designed to handle next-generation sequencing data, specifically targeting nonrecombining haploid genomic regions.
  • Performance was assessed using simulated data and real human Y-chromosome data from related individuals.

Main Results:

  • IMPUTOR successfully imputes up to 95% of missing sites and corrects up to 81% of sequencing errors under optimal conditions.
  • The software demonstrates high accuracy in detecting induced mutations without making erroneous imputations or corrections.
  • Validation with human Y-chromosome data confirmed IMPUTOR's efficacy in real-world applications.

Conclusions:

  • IMPUTOR provides an efficient and accurate solution for imputing missing and correcting erroneous genotypes in haploid nonrecombining genomic data.
  • The phylogenetically aware approach enhances the reliability of genomic data, particularly from next-generation sequencing.
  • IMPUTOR is a valuable tool for researchers working with challenging genomic datasets, such as human Y-chromosome sequences.