use COSMIC

To use COSMIC v76 with WGSA06:

1. Create a folder named "COSMIC" under resources.

2. Obtain a copy of the GRCH37 version of the CosmicCodingMuts.vcf.gz from COSMIC.

   • register an account at COSMIC using your email address

   • sftp "your_email_address"@sftp-cancer.sanger.ac.uk

   • sftp> get /cosmic/grch37/cosmic/v76/VCF/CosmicCodingMuts.vcf.gz

3. Put the the file CosmicCodingMuts.vcf.gz in the COSMIC folder.

4. In the configuration file, choose s(np), i(ndel) or b(oth) in the option line beginning with "COSMIC:".