Given a VCF file annotated with both dbSNP and COSMIC, it removes the SNPs present in the CosmicCodingMuts84.vcf or CosmicNonCodingVariants.vcf files. The problem comes from the fact that the VCF annotated with dbSNP contains SNPs that could also be genetically dangerous and they should not be thrown-away.

The COSMIC VCFs, both the coding and non coding, are not freely available for everyone. You should sign up to COSMIC using your university email. COSMIC data is completely free to academic research communities, but commercial users should contact COSMIC for licences which are priced according to organisation size.

It uses uthash, a hash table for C structures using COSMIC IDS as keys.

The VCF to be filtered shoud be annotated with COSMIC using SnpSift software:

$ java -Xmx4g -jar /tmp/snpEff/SnpSift.jar annotate All_20180418.vcf.gz  starting.vcf  > dbsnp_annotated.vcf
$ java -Xmx4g -jar /tmp/snpEff/SnpSift.jar annotate CosmicCodingMuts.vcf.gz  dbsnp_annotated.vcf  > cosmic_annotated.vcf

Then you can use the program:

$ cosmic_snp_filter CosmicNonCodingVariants.vcf cosmic_annotated.vcf > cosmic_annotated_with_no_snps.vcf

The -h options shows the help:

$ cosmic_snp_filter -h
Usage: cosmic_snp_filter  [OPTION]... COSMIC_VCF VCF_to_filter
  -h	show help options

DO WHAT THE FUCK YOU WANT TO PUBLIC LICENSE, version 2, December 2004.