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A program that finds single‐base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. SomaticCall takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations).

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
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  • (Spencer et al., 2014) Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. The Journal of molecular diagnostics.
    PMID: 24211364
  • (Stead et al., 2013) Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Human mutation.
    PMID: 23766071
  • (Roberts et al., 2013) A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics.
    PMID: 23842810
  • (Wang et al., 2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome medicine.
    PMID: 24112718

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