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Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
BACKGROUND: Inherent 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 m...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293637/ https://www.ncbi.nlm.nih.gov/pubmed/30545283 http://dx.doi.org/10.1186/s12711-018-0436-4 |
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author | Ros-Freixedes, Roger Battagin, Mara Johnsson, Martin Gorjanc, Gregor Mileham, Alan J. Rounsley, Steve D. Hickey, John M. |
author_facet | Ros-Freixedes, Roger Battagin, Mara Johnsson, Martin Gorjanc, Gregor Mileham, Alan J. Rounsley, Steve D. Hickey, John M. |
author_sort | Ros-Freixedes, Roger |
collection | PubMed |
description | BACKGROUND: Inherent 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. RESULTS: We 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. CONCLUSIONS: We 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. |
format | Online Article Text |
id | pubmed-6293637 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-62936372018-12-18 Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing Ros-Freixedes, Roger Battagin, Mara Johnsson, Martin Gorjanc, Gregor Mileham, Alan J. Rounsley, Steve D. Hickey, John M. Genet Sel Evol Research Article BACKGROUND: Inherent 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. RESULTS: We 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. CONCLUSIONS: We 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. BioMed Central 2018-12-13 /pmc/articles/PMC6293637/ /pubmed/30545283 http://dx.doi.org/10.1186/s12711-018-0436-4 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Ros-Freixedes, Roger Battagin, Mara Johnsson, Martin Gorjanc, Gregor Mileham, Alan J. Rounsley, Steve D. Hickey, John M. Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
title | Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
title_full | Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
title_fullStr | Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
title_full_unstemmed | Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
title_short | Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
title_sort | impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293637/ https://www.ncbi.nlm.nih.gov/pubmed/30545283 http://dx.doi.org/10.1186/s12711-018-0436-4 |
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