Version: cisCall v7.2.1-p-rc0


cisCall is a variant caller specialized for identifying DNA alterations of FFPE samples in clinical sequencing.

cisCall7 is the latest version of cisCall developed as a command-line tool, and contains the following variant caller modules:

  • cisMuton
    • caller for SNV/indel
  • cisCton
    • caller for copy number alteration
  • cisFusion
    • caller for fusion gene


  • 2020-05-08:
    • v7.2.1-p-rc0 released
      • Fix bugs
      • Deprecate TARGET and WEXOME mapping mode
  • 2019-12-09:
    • v7.2.0-p released
      • Enable the modules to detect more types of variants
        • cisMuton
          • MNV (Multiple Nucleotide Variant)
        • cisCton
          • copy number loss
        • cisFusion
          • structural variants
            • long deletion
            • inversion
            • tandem duplication
      • Improve variant filters
      • Improve logging
      • Improve parallelization
      • Use BWA-MEM for read mapping
      • Use Samtools for duplicate removal
      • Update the names of output files and directories
      • Update the options
      • Fix bugs
  • 2018-10-05:
    • v7.2.0-p-rc4 released
      • Improve algorithms and parameters of false positive SNV/Indel filters (Surrounded and VAFlees)
      • Deprecate --free-memory-rate
      • Fix bugs


Send a request to download cisCall7 from the form at the following page:

Getting started