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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

nPoRe: n-polymer realigner for improved pileup-based variant calling.

Tim Dunn¹, David Blaauw², Reetuparna Das²

¹University of Michigan, Ann Arbor, USA. timdunn@umich.edu.

BMC Bioinformatics

|March 17, 2023

Summary

Improving germline variant calling for insertions and deletions (INDELs) using nanopore sequencing is crucial. New alignment methods enhance INDEL recall by accurately handling homopolymers and tandem repeats, boosting accuracy in genetic analysis.

Keywords:

Alignment Copy number Germline variant calling Homopolymer N-polymer Nanopore sequencing Short tandem repeat Variable gap penalty

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Area of Science:

Genomics
Bioinformatics

Background:

Nanopore sequencing offers rapid genomic data generation.
Current nanopore basecalling has high accuracy for single nucleotide polymorphisms (SNPs) but struggles with insertions and deletions (INDELs).
INDEL recall remains below 80% for standard R9.4.1 flow cells, limiting comprehensive germline variant analysis.

Purpose of the Study:

To improve the accuracy of germline INDEL variant calling from nanopore sequencing data.
To develop enhanced alignment algorithms for better detection of INDELs, particularly in repetitive regions.

Main Methods:

Extension of the Needleman-Wunsch affine gap alignment algorithm.
Introduction of novel gap penalties specifically designed for homopolymers and tandem repeats.
Application of haplotype phasing and realignment techniques to nanopore sequencing reads.

Main Results:

Haplotype phasing improved INDEL recall from 63.76% to [Formula: see text] at consistent precision.
Further improvement in INDEL recall to [Formula: see text] was achieved using nPoRe realignment.
The enhanced alignment demonstrated superior accuracy in regions with repetitive sequences.

Conclusions:

Read phasing and realignment significantly enhance INDEL recall in nanopore sequencing data.
Modified gap penalties in alignment are effective for accurately calling INDELs in homopolymers and tandem repeats.
These advancements address a key limitation in nanopore-based germline variant calling, improving genomic analysis.