ORIGINAL RESEARCH

The impact of sequencing depth on accuracy of single nucleotide variant calls

About authors

Genotek Inc., Moscow

Correspondence should be addressed: Valery Ilyinsky
per. Nastavnichesky, d. 17, str. 1, Moscow, Russia, 105120; ur.ketoneg@yrelav

About paper

Acknowledgements: the authors thank Anna Davydova of Genotek for her helpful comments.

All authors' contribution to this work is equal: selection and analysis of literature, planning of the manuscript's structure, data interpretation, drafting of the manuscript, editing.

Received: 2017-06-22 Accepted: 2017-06-27 Published online: 2017-07-19
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Today, next generation sequencing (NGS) is extensively used in the research setting. However, high costs of NGS testing still prevent its routine use in clinical practice. One of the factors affecting the cost of sequencing is the number of reads per site, i.e. the number of times each nucleotide gets sequenced. On the one hand, lower coverage makes the whole process much faster and less time-consuming. On the other hand, it results in poor data quality. No unanimous opinion has been reached yet as to what minimum depth of coverage can produce reliable results. The aim of this study was to determine the minimum number of reads sufficient for accurate base calling of heterozygous and single nucleotide variants (SNV). Using bioinformatics methods, we demonstrate that accuracy can be achieved at a minimum depth of 12x.

Keywords: next generation sequencing, sequencing depth, mutation, read, SNP, SNV

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