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Related Experiment Video

Updated: Dec 2, 2025

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

read_haps: using read haplotypes to detect same species contamination in DNA sequences.

Hannes P Eggertsson¹, Bjarni V Halldorsson^1,2

¹deCODE Genetics, Reykjavík 102, Iceland.

Bioinformatics (Oxford, England)

|November 2, 2020

Summary

Detecting DNA contamination is crucial for reliable genetic analysis. The read_haps tool identifies contamination in short read whole genome sequencing data by detecting three haplotypes between single nucleotide polymorphisms.

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Area of Science:

Genetics
Bioinformatics

Background:

Reliable data analysis is fundamental in genetics.
Sample contamination is a common issue in biological research, potentially compromising results.

Purpose of the Study:

To introduce a novel tool for detecting DNA contamination in sequencing data.
To address the challenge of ubiquitous sample contamination in biological studies.

Main Methods:

The study presents `read_haps`, a computational tool designed for contamination detection.
The method leverages the presence of three haplotypes between polymorphic single nucleotide polymorphisms (SNPs) in diploid species.

Main Results:

`read_haps` effectively detects sample contamination from whole genome sequencing data.
The tool is applicable to human and other diploid organisms.

Conclusions:

`read_haps` provides a reliable method for verifying sample integrity in genetic studies.
Ensuring data quality through contamination detection is essential for accurate genomic research.