Introduction

Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research.

Publications

  1. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.
    Cite this
    Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett JC, Dry JR, 2016-06-01 - Nucleic acids research

Credits

  1. Zhongwu Lai
    Developer

    Oncology iMed, AstraZeneca, United States of America

  2. Aleksandra Markovets
    Developer

    Oncology iMed, AstraZeneca, United States of America

  3. Miika Ahdesmäki
    Developer

    Oncology iMed, AstraZeneca, United States of America

  4. Brad Chapman
    Developer

    Bioinformatics Core, Harvard T.H. Chan School of Public Health, United States of America

  5. Oliver Hofmann
    Developer

    Bioinformatics Core, Harvard T.H. Chan School of Public Health, United States of America

  6. Robert McEwen
    Developer

    Oncology iMed, AstraZeneca, United States of America

  7. Justin Johnson
    Developer

    Oncology iMed, AstraZeneca, United States of America

  8. Brian Dougherty
    Developer

    Oncology iMed, AstraZeneca, United States of America

  9. J Carl Barrett
    Developer

    Oncology iMed, AstraZeneca, United States of America

  10. Jonathan R Dry
    Investigator

    Oncology iMed, AstraZeneca, United States of America

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Summary
AccessionBT004063
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJonathan R Dry