Cosmic database update issue in annovar

Question

[abhijitswain]

When I tried to update the cosmic v101 for annovar database I got following error :

prepare_annovar_user.pl -dbtype cosmic Cosmic_GenomeScreensMutant_v101_GRCh37.tsv -vcf Cosmic_GenomeScreensMutant_v101_GRCh37.vcf > hg19_cosmic101.txt 
> NOTICE: Finished reading 13601142 mutation ID from the VCF file Cosmic_GenomeScreensMutant_v101_GRCh37.vcf
> Error: COSMIC MutantExport format error: column 17 or 18 or 12 should be 'Mutation ID' or 'GENOMIC_MUTATAION_ID' or 'ID_NCV'

[Ahmed]

Ensure that the cosmic input files are not compressed. Also, Try using following prepare_annovar_user.pl:

http://www.openbioinformatics.org/annovar/download/prepare_annovar_user.pl