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

Bioinformatics

Volumn 29, Issue 17, 2013, Pages 2208-2210

  Rashid, Mamunur ^a   Robles Espinoza, Carla Daniela ^a   Rust, Alistair G ^a   Adams, David J ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BREAST TUMOR; COMPUTER PROGRAM; EXOME; FEMALE; GENETIC VARIABILITY; GENETICS; GENOME; GENOMICS; HUMAN; LIVER CELL CARCINOMA; LIVER TUMOR; NEOPLASM; PROCEDURES; ARTICLE; METHODOLOGY;

ALGORITHMS; BREAST NEOPLASMS; CARCINOMA, HEPATOCELLULAR; EXOME; FEMALE; GENETIC VARIATION; GENOME; GENOMICS; HUMANS; LIVER NEOPLASMS; NEOPLASMS; SOFTWARE;

EID: 84882618092     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt371     Document Type: Article

References (7)

1. Edmonson, M. N. et al. (2011) Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics, 27, 865-866.
2. Guichard, C. et al. (2012) Integrated analysis of somatic mutations and focal copynumber changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet., 44, 694-698.
3. Koboldt, D. C. et al. (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res., 22, 568-576.
4. Li, H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
5. Sherry, S. T. et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
6. Stephens, P. J. et al. (2012) The landscape of cancer genes and mutational processes in breast cancer. Nature, 486, 400-404.
7. The 1000 Genomes Project Consortium et al. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.