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A beginners guide to SNP calling from high-throughput DNA-sequencing data

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Abstract

High-throughput DNA sequencing (HTS) is of increasing importance in the life sciences. One of its most prominent applications is the sequencing of whole genomes or targeted regions of the genome such as all exonic regions (i.e., the exome). Here, the objective is the identification of genetic variants such as single nucleotide polymorphisms (SNPs). The extraction of SNPs from the raw genetic sequences involves many processing steps and the application of a diverse set of tools. We review the essential building blocks for a pipeline that calls SNPs from raw HTS data. The pipeline includes quality control, mapping of short reads to the reference genome, visualization and post-processing of the alignment including base quality recalibration. The final steps of the pipeline include the SNP calling procedure along with filtering of SNP candidates. The steps of this pipeline are accompanied by an analysis of a publicly available whole-exome sequencing dataset. To this end, we employ several alignment programs and SNP calling routines for highlighting the fact that the choice of the tools significantly affects the final results.

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Acknowledgments

The work of MP was supported by an intramural grant from the Medical Faculty of the University at Lübeck.

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  1. André Altmann

    Present address: Functional Imaging in Neuropsychiatric Disorders Laboratory, Stanford University School of Medicine, 780 Welch Road, Suite 105, Palo Alto, CA, 94304, USA

Authors and Affiliations

  1. Statistical Genetics, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany

    André Altmann & Bertram Müller-Myhsok

  2. Molecular Genetics of Affective Disorder, Max Planck Institute of Psychiatry, Munich, Germany

    Peter Weber, Daniel Bader & Elisabeth B. Binder

  3. Genetic Epidemiology, Institut für Medizinische Biometrie und Statistik, University of Lübeck, Lübeck, Germany

    Michael Preuß

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  1. André Altmann
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Altmann, A., Weber, P., Bader, D. et al. A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet 131, 1541–1554 (2012). https://doi.org/10.1007/s00439-012-1213-z

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