Title |
ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets
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Published in |
Source Code for Biology and Medicine, January 2014
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DOI | 10.1186/1751-0473-9-3 |
Pubmed ID | |
Authors |
Bernard J Pope, Tú Nguyen-Dumont, Fleur Hammet, Daniel J Park |
Abstract |
We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles underly ROVER software (derived from Read Overlap PCR-MPS variant caller), which we have recently used to report the screening for genetic mutations in the breast cancer predisposition gene PALB2. Here, we describe the algorithms underlying ROVER and its usage. |
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Geographical breakdown
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China | 1 | 50% |
Unknown | 1 | 50% |
Demographic breakdown
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Members of the public | 1 | 50% |
Scientists | 1 | 50% |
Mendeley readers
Geographical breakdown
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Unknown | 18 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 4 | 22% |
Researcher | 4 | 22% |
Student > Postgraduate | 2 | 11% |
Student > Bachelor | 1 | 6% |
Student > Master | 1 | 6% |
Other | 3 | 17% |
Unknown | 3 | 17% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 4 | 22% |
Computer Science | 4 | 22% |
Agricultural and Biological Sciences | 4 | 22% |
Medicine and Dentistry | 2 | 11% |
Unknown | 4 | 22% |