Cosmic Database using BioMart

Question

[noeD]

Hello!

I have read that with BioMart package in R it is possible to download the cosmic database. Unfortunately I didn't understand how to do it. If I use listMart() I see only ensemble-database.. I have tried with listMart(host=http://cancer.sanger.ac.uk/cosmic), but it didn't work...

Thank you in advance for you help

Best

Answer 1

[Emily]

You use the Ensembl variation somatic variation database to access COSMIC data:

cosmicMart = useEnsembl (biomart="snp", dataset = hsapiens_snp_som")

If you're looking to download the whole COSMIC database, BioMart is not a suitable way to do this. Please download the somatic VCF files from the FTP site instead: ftp://ftp.ensembl.org/pub/current_variation/vcf/homo_sapiens/

[noeD]

Thank you for your reply. But is it possible to download the database for INDEL mutations?

Thank you in advance

[Emily]

You might be best downloading the VCF then using vcf-tools to filter