Introduction

Recent advances in high-throughput sequencing technologies have enabled us to sequence large number of cancer samples to reveal novel insights into oncogenetic mechanisms. However, the presence of intratumoral heterogeneity, normal cell contamination and insufficient sequencing depth, together pose a challenge for detecting somatic mutations. Here we propose a fast and an accurate somatic single-nucleotide variations (SNVs) detection program, FaSD-somatic. The performance of FaSD-somatic is extensively assessed on various types of cancer against several state-of-the-art somatic SNV detection programs. Benchmarked by somatic SNVs from either existing databases or de novo higher-depth sequencing data, FaSD-somatic has the best overall performance. Furthermore, FaSD-somatic is efficient, it finishes somatic SNV calling within 14 h on 50X whole genome sequencing data in paired samples.The program, datasets and supplementary files are available at http://jjwanglab.org/FaSD-somatic/.Supplementary data are available at Bioinformatics online.

Publications

  1. FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.
    Cite this
    Wang W, Wang P, Xu F, Luo R, Wong MP, Lam TW, Wang J, 2014-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Weixin Wang
    Developer

    Department of Biochemistry, LKS Faculty of Medicine, China

  2. Panwen Wang
    Developer

    Department of Biochemistry, LKS Faculty of Medicine, China

  3. Feng Xu
    Developer

    Department of Biochemistry, LKS Faculty of Medicine, China

  4. Ruibang Luo
    Developer

    Department of Biochemistry, LKS Faculty of Medicine, China

  5. Maria Pik Wong
    Developer

    Department of Biochemistry, LKS Faculty of Medicine, China

  6. Tak-Wah Lam
    Developer

    Department of Biochemistry, LKS Faculty of Medicine, China

  7. Junwen Wang
    Investigator

    Department of Biochemistry, LKS Faculty of Medicine, China

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Summary
AccessionBT000083
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByJunwen Wang