Introduction

Extensive DNA sequencing of tumor and matched normal samples using exome and whole-genome sequencing technologies has enabled the discovery of recurrent genetic alterations in cancer cells, but variability in stromal contamination and subclonal heterogeneity still present a severe challenge to available detection algorithms.Here, we describe publicly available software, Shimmer, which accurately detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. This program produces somatic single-nucleotide variant predictions with significantly higher sensitivity and accuracy than other available software when run on highly contaminated or heterogeneous samples, and it gives comparable sensitivity and accuracy when run on samples of high purity.http://www.github.com/nhansen/Shimmer

Publications

  1. Shimmer: detection of genetic alterations in tumors using next-generation sequence data.
    Cite this
    Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC, 2013-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Nancy F Hansen
    Developer

    Genome Technology Branch, NHGRI/NIH

  2. Jared J Gartner
    Developer

  3. Lan Mei
    Developer

  4. Yardena Samuels
    Developer

  5. James C Mullikin
    Investigator

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Summary
AccessionBT006792
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJames C Mullikin