CRAB is a collection of data from a variety of cancer databases that has been parsed and summarized into BED or VCF file formats to be used easily with vcfanno for the annotation of VCF files. CRAB was designed to be used alongside OncoGEMINI, but provides a useful resource that can be useful in other applications.
Available files through the CRAB are designed to be easily used alongside vcfanno to add annotations to VCF files. To quickly get started with vcfanno, the following is required:
- Download and install vcfanno (for directions refer to the repo)
- The source file(s) containing the annotation information that is desired to be added to a VCF (generally a BED or VCF file(s)).
- A vcfanno configuration file that directs vcfanno to the source file(s) and the desired information within the source file(s) (and designations for them) for annotation.
We have provided an example vcfanno configuration file that will annotate a VCF with information that has been parsed from CIViC and the CGI. To use this configuration file, download it as well as the source files it uses from CIViC and CGI:
- vcfanno.conf
- civic_genes_summaries.bed.gz
- civic_variants_summaries.bed.gz
- ccg.bed.gz
- onco_muts.bed.gz
Once the files are downloaded be sure to specify the paths to the CIViC and CGI files in the vcfanno.conf file. With vcfanno installed and all the files in place, annotate a VCF with vcfanno using a single command:
vcfanno vcfanno.config your.vcf.gz > your_annotated.vcf.gz
Any number of files can be added to the vcfanno configuration file enabling great customization to the specific types and quantity of annotations that can be added to a VCF file.