ArticleGenetics, selection, evolution : GSE2018
Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing.
Article in Genetics, selection, evolution : GSE, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 70 citations in OpenAlex.
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- Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation.BMC genomics · 2024Article
- Genomic reproducibility in the bioinformatics era.Genome biology · 2024Review
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus.Marine biotechnology (New York, N.Y.) · 2023Article
- Reciprocal influence of soil, phyllosphere, and aphid microbiomes.Environmental microbiome · 2023Article
- Rapid and easy construction of a simplified amplicon sequencing (simplified AmpSeq) library for marker-assisted selection.Scientific reports · 2023Article
- Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale.Royal Society open science · 2023Article
- Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.Cells · 2023Review
- Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.Genetics, selection, evolution : GSE · 2022Article
- Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol.Molecular ecology resources · 2022Article
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
- Genomic prediction with whole-genome sequence data in intensely selected pig lines.Genetics, selection, evolution : GSE · 2022Article
- Rare and population-specific functional variation across pig lines.Genetics, selection, evolution : GSE · 2022Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
Abstract
backgroundInherent sources of error and bias that affect the quality of sequence data include index hopping and bias towards the reference allele. The impact of these artefacts is likely greater for low-coverage data than for high-coverage data because low-coverage data has scant information and many standard tools for processing sequence data were designed for high-coverage data. With the proliferation of cost-effective low-coverage sequencing, there is a need to understand the impact of these errors and bias on resulting genotype calls from low-coverage sequencing.
resultsWe used a dataset of 26 pigs sequenced both at 2× with multiplexing and at 30× without multiplexing to show that index hopping and bias towards the reference allele due to alignment had little impact on genotype calls. However, pruning of alternative haplotypes supported by a number of reads below a predefined threshold, which is a default and desired step of some variant callers for removing potential sequencing errors in high-coverage data, introduced an unexpected bias towards the reference allele when applied to low-coverage sequence data. This bias reduced best-guess genotype concordance of low-coverage sequence data by 19.0 absolute percentage points.
conclusionsWe propose a simple pipeline to correct the preferential bias towards the reference allele that can occur during variant discovery and we recommend that users of low-coverage sequence data be wary of unexpected biases that may be produced by bioinformatic tools that were designed for high-coverage sequence data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.