Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes

Bioinformatics. 2013 Sep 1;29(17):2208-10. doi: 10.1093/bioinformatics/btt371. Epub 2013 Jun 25.


We have developed Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application. Availabilty: Cake is open-source and is available from

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Breast Neoplasms / genetics
  • Carcinoma, Hepatocellular / genetics
  • Exome
  • Female
  • Genetic Variation*
  • Genome
  • Genomics / methods
  • Humans
  • Liver Neoplasms / genetics
  • Neoplasms / genetics*
  • Software*