COSMIC (Catalogue of Somatic Mutations in Cancer) is a data resource that is designed to store and display somatic mutation information and related details and contains information relating to human cancers. Data in COSMIC is curated from known Cancer Genes Literature and Systematic Screens. COSMIC data is freely downloadable in many formats on the project's FTP site: ftp://ftp.sanger.ac.uk/pub/CGP/cosmic.

If you use COSMIC annotations, please credit the project with the following acknowledgement:

The mutation data was obtained from the Sanger Institute Catalogue Of Somatic Mutations In Cancer web site, http://www.sanger.ac.uk/cosmic. Bamford et al (2004). The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer, 91,355-358.

There are 3 data sources that you can use to annotate vtools project variants with those from the COSMIC project. There are 2 higher-level databases that annotate variants with information such as how many cancer samples have been documented to contain the variant. These databases include a database that annotates coding mutations (CosmicCodingMuts) and a database that annotates noncoding variants (CosmicNonCodingVariants).

There is also a more detailed database (CosmicMutantExport) that can be linked to these higher-level databases (e.g., vtools use CosmicMutantExport --linkedby CosmicCodingMuts.COSMIC_ID or vtools use CosmicMutantExport --linked_by CosmicNonCodingVariants.COSMIC_ID) to extract detailed information about the COSMIC variant (such as variant details and details of the samples the variant was detected in). See below for the available annotation fields from these databases.

% vtools use CosmicCodingMuts
% vtools show annotation CosmicCodingMuts -v2
Annotation database CosmicCodingMuts (version v61_260912)
Description: Cosmic coding mutation database.  This data contains mutations 
affecting 10 or less nucleotides in REF.  The mutation data was obtained 
from the Sanger Institute Catalogue Of Somatic Mutations In Cancer web site, 
http://www.sanger.ac.uk/cosmic.  Bamford et al (2004). The COSMIC (Catalogue 
of Somatic Mutations in Cancer) database and website. Br J Cancer, 91,355-358.
Database type: variant
Number of records: 216,900
Number of distinct variants: 198,331
Reference genome hg19: ['chr', 'pos', 'ref', 'alt']

Field:           chr
Type:            string
Comment:         Chromosome
Missing entries: 0 
Unique Entries:  25

Field:           pos
Type:            integer
Comment:         1-based position
Missing entries: 0 
Unique Entries:  193,076
Range:           8115 - 249212084

Field:           COSMIC_ID
Type:            string
Comment:         cosmic id of mutation
Missing entries: 0 
Unique Entries:  216,900

Field:           ref
Type:            string
Comment:         Reference allele, '-' for insertion.
Missing entries: 0 
Unique Entries:  1,241

Field:           alt
Type:            string
Comment:         Alternative allele, '-' for deletion.
Missing entries: 0 
Unique Entries:  1,138

Field:           gene
Type:            string
Comment:         genename
Missing entries: 0 
Unique Entries:  20,405

Field:           strand
Type:            string
Comment:         strand
Missing entries: 0 
Unique Entries:  2

Field:           CDS
Type:            string
Comment:         CDS annotation
Missing entries: 0 
Unique Entries:  65,794

Field:           AA
Type:            string
Comment:         Peptide annotation
Missing entries: 0 
Unique Entries:  111,311

Field:           CNT
Type:            integer
Comment:         Number of samples with this mutation
Missing entries: 0 
Unique Entries:  157
Range:           1 - 29906
% vtools use CosmicNonCodingVariants
% vtools show annotation CosmicNonCodingVariants -v2
Annotation database CosmicNonCodingVariants (version v61_260912)
Description: Cosmic non-coding mutation database.  This data contains 
mutations affecting 10 or less nucleotides in REF.  The mutation data 
was obtained from the Sanger Institute Catalogue Of Somatic Mutations 
In Cancer web site, http://www.sanger.ac.uk/cosmic.  Bamford et al 
(2004). The COSMIC (Catalogue of Somatic Mutations in Cancer) database 
and website. Br J Cancer, 91,355-358.
Database type: variant
Number of records: 108,713
Number of distinct variants: 104,410
Reference genome hg19: ['chr', 'pos', 'ref', 'alt']

Field:           chr
Type:            string
Comment:         Chromosome
Missing entries: 0 
Unique Entries:  24

Field:           pos
Type:            integer
Comment:         1-based position
Missing entries: 0 
Unique Entries:  104,370
Range:           13663 - 249204167

Field:           COSMIC_ID
Type:            string
Comment:         cosmic id of mutation
Missing entries: 0 
Unique Entries:  108,713

Field:           ref
Type:            string
Comment:         Reference allele, '-' for insertion.
Missing entries: 0 
Unique Entries:  1,251

Field:           alt
Type:            string
Comment:         Alternative allele, '-' for deletion.
Missing entries: 0 
Unique Entries:  152

Field:           gene
Type:            string
Comment:         genename
Missing entries: 88,900 (81.8% of 108,713 records)
Unique Entries:  7,501

Field:           strand
Type:            string
Comment:         strand
Missing entries: 88,900 (81.8% of 108,713 records)
Unique Entries:  2
% vtools use CosmicMutantExport --linked_by CosmicCodingMuts.COSMIC_ID
% vtools show annotation CosmicMutantExport -v2
Annotation database CosmicMutantExport (version v61_260912)
Description: Cosmic mutant export.  This data contains all coding 
point mutations.  The mutation data was obtained from the Sanger 
Institute Catalogue Of Somatic Mutations In Cancer web site, 
http://www.sanger.ac.uk/cosmic.  Bamford et al (2004). The 
COSMIC (Catalogue of Somatic Mutations in Cancer) database and 
website. Br J Cancer, 91,355-358.
Database type: field
Number of records: 404,865
Number of distinct entries: 224,650
Reference genome *: ['COSMIC_ID']

Field:           COSMIC_ID
Type:            string
Missing entries: 0 
Unique Entries:  224,650

Field:           Gene_name
Type:            string
Missing entries: 0 
Unique Entries:  20,451

Field:           Accession_Number
Type:            string
Missing entries: 0 
Unique Entries:  20,403

Field:           Gene_CDS_length
Type:            string
Missing entries: 0 
Unique Entries:  2,220

Field:           HGNC_ID
Type:            string
Missing entries: 0 
Unique Entries:  16,990

Field:           Sample_name
Type:            string
Missing entries: 0 
Unique Entries:  179,301

Field:           ID_sample
Type:            string
Missing entries: 0 
Unique Entries:  183,630

Field:           ID_tumour
Type:            string
Missing entries: 0 
Unique Entries:  181,851

Field:           Primary_site
Type:            string
Missing entries: 0 
Unique Entries:  44

Field:           Site_subtype
Type:            string
Missing entries: 0 
Unique Entries:  185

Field:           Primary_histology
Type:            string
Missing entries: 0 
Unique Entries:  91

Field:           Histology_subtype
Type:            string
Missing entries: 0 
Unique Entries:  417

Field:           Genomewide_screen
Type:            string
Missing entries: 0 
Unique Entries:  3

Field:           Mutation_ID
Type:            string
Missing entries: 0 
Unique Entries:  224,650

Field:           Mutation_CDS
Type:            string
Missing entries: 0 
Unique Entries:  69,434

Field:           Mutation_AA
Type:            string
Missing entries: 0 
Unique Entries:  115,530

Field:           Mutation_Description
Type:            string
Missing entries: 0 
Unique Entries:  17

Field:           Mutation_zygosity
Type:            string
Missing entries: 0 
Unique Entries:  4

Field:           Mutation_NCBI36_genome_position
Type:            string
Missing entries: 0 
Unique Entries:  35,240

Field:           Mutation_NCBI36_strand
Type:            string
Missing entries: 0 
Unique Entries:  4

Field:           Mutation_GRCh37_genome_position
Type:            string
Missing entries: 0 
Unique Entries:  198,031

Field:           Mutation_GRCh37_strand
Type:            string
Missing entries: 0 
Unique Entries:  4

Field:           Mutation_somatic_status
Type:            string
Missing entries: 0 
Unique Entries:  7

Field:           Pubmed_PMID
Type:            string
Missing entries: 0 
Unique Entries:  7,690

Field:           Sample_source
Type:            string
Missing entries: 0 
Unique Entries:  30

Field:           Tumour_origin
Type:            string
Missing entries: 0 
Unique Entries:  9

Field:           Comments
Type:            string
Missing entries: 0 
Unique Entries:  3,202