An SVM-based approach for genotyping deletions and insertions with population sequence reads

Chong Chu; Jin Zhang; Yufeng Wu

doi:10.1109/ICCABS.2013.6629219

An SVM-based approach for genotyping deletions and insertions with population sequence reads

Chong Chu, Jin Zhang, Yufeng Wu

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Because of the low quality and large size of population sequence data, calling population structural variations (SVs) genotypes is still a challenging problem. In this paper, we propose an SVM-based approach for genotyping deletion and insertion polymorphisms with population sequence reads. The key idea of our approach is combining multiple sources of information contained in sequence data in calling genotypes. Results on both simulated and real data suggest that our approach works well.

Original language	English
Title of host publication	2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013
DOIs	https://doi.org/10.1109/ICCABS.2013.6629219
State	Published - 2013
Event	2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013 - New Orleans, LA, United States Duration: Jun 12 2013 → Jun 14 2013

Publication series

Name	2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013

Conference

Conference	2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013
Country/Territory	United States
City	New Orleans, LA
Period	06/12/13 → 06/14/13

Keywords

genotype calling
high-throughput sequencing
structural variation

Access to Document

10.1109/ICCABS.2013.6629219

Cite this

Chu, C., Zhang, J., & Wu, Y. (2013). An SVM-based approach for genotyping deletions and insertions with population sequence reads. In 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013 Article 6629219 (2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013). https://doi.org/10.1109/ICCABS.2013.6629219

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title = "An SVM-based approach for genotyping deletions and insertions with population sequence reads",

abstract = "Because of the low quality and large size of population sequence data, calling population structural variations (SVs) genotypes is still a challenging problem. In this paper, we propose an SVM-based approach for genotyping deletion and insertion polymorphisms with population sequence reads. The key idea of our approach is combining multiple sources of information contained in sequence data in calling genotypes. Results on both simulated and real data suggest that our approach works well.",

keywords = "genotype calling, high-throughput sequencing, structural variation",

author = "Chong Chu and Jin Zhang and Yufeng Wu",

year = "2013",

doi = "10.1109/ICCABS.2013.6629219",

language = "English",

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series = "2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013",

booktitle = "2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013",

note = "2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013 ; Conference date: 12-06-2013 Through 14-06-2013",

}

Chu, C, Zhang, J & Wu, Y 2013, An SVM-based approach for genotyping deletions and insertions with population sequence reads. in 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013., 6629219, 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013, 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013, New Orleans, LA, United States, 06/12/13. https://doi.org/10.1109/ICCABS.2013.6629219

An SVM-based approach for genotyping deletions and insertions with population sequence reads. / Chu, Chong; Zhang, Jin; Wu, Yufeng.
2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013. 2013. 6629219 (2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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N2 - Because of the low quality and large size of population sequence data, calling population structural variations (SVs) genotypes is still a challenging problem. In this paper, we propose an SVM-based approach for genotyping deletion and insertion polymorphisms with population sequence reads. The key idea of our approach is combining multiple sources of information contained in sequence data in calling genotypes. Results on both simulated and real data suggest that our approach works well.

AB - Because of the low quality and large size of population sequence data, calling population structural variations (SVs) genotypes is still a challenging problem. In this paper, we propose an SVM-based approach for genotyping deletion and insertion polymorphisms with population sequence reads. The key idea of our approach is combining multiple sources of information contained in sequence data in calling genotypes. Results on both simulated and real data suggest that our approach works well.

KW - genotype calling

KW - high-throughput sequencing

KW - structural variation

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M3 - Conference contribution

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SN - 9781479907144

T3 - 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013

BT - 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013

T2 - 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013

Y2 - 12 June 2013 through 14 June 2013

ER -

Chu C, Zhang J, Wu Y. An SVM-based approach for genotyping deletions and insertions with population sequence reads. In 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013. 2013. 6629219. (2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2013). doi: 10.1109/ICCABS.2013.6629219

An SVM-based approach for genotyping deletions and insertions with population sequence reads

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