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Chronic Lymphocytic Leukemia pp 277–318Cite as

Bioinformatics Analysis of Whole Exome Sequencing Data

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1881))

Abstract

This chapter contains a step-by-step protocol for identifying somatic SNPs and small Indels from next-generation sequencing data of tumor samples and matching normal samples. The workflow presented here is largely based on the Broad Institute’s “Best Practices” guidelines and makes use of their Genome Analysis Toolkit (GATK) platform. Variants are annotated with population allele frequencies and curated resources such as GnomAD and ClinVar and curated effect predictions from dbNSFP using VCFtools, SnpEff, and SnpSift.

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Acknowledgments

The authors would like to thank the institutions, developers, and documenters of the informatics tools used in this chapter’s workflows. Genomics and disease research in general benefits hourly from the availability of tools such as Bioconda, BWA, GATK, HaplotypeCaller, Mutect2, Samtools, SNPEff , VarScan, and Vcftools, as well as public resources such as ClinVar and GnomAD.

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Authors and Affiliations

  1. BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI, USA

    Peter J. Ulintz, Weisheng Wu & Chris M. Gates

  2. Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA

    Peter J. Ulintz

Authors
  1. Peter J. Ulintz
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  2. Weisheng Wu
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  3. Chris M. Gates
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Corresponding author

Correspondence to Peter J. Ulintz .

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Editors and Affiliations

  1. Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA

    Sami N. Malek

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Ulintz, P.J., Wu, W., Gates, C.M. (2019). Bioinformatics Analysis of Whole Exome Sequencing Data. In: Malek, S. (eds) Chronic Lymphocytic Leukemia. Methods in Molecular Biology, vol 1881. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8876-1_21

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  • DOI: https://doi.org/10.1007/978-1-4939-8876-1_21

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8875-4

  • Online ISBN: 978-1-4939-8876-1

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