Please update prepare_annovar_user for COSMIC v.91-92

[RKV82]

Dear Prof. Wang!

I've tried to convert COSMIC tsv files to ANNOVAR, but encountered the same problem as in Issue #77

Could you update prepare_annovar_user.pl to handle the COSMIC v91 and upcoming v92

Thanks in advance.

[ArshiyaG]

Hey @RKV82 ,

Unzip the cosmic tsv file and try running the command again. It worked for me

[RKV82]

Unzip the cosmic tsv file and try running the command again. It worked for me

Thanks, but for GenomeScreenMutant it still not work. Solved by cut -f 1-16,18-39

[kaichop]

@RKV82 Thank you, if I understand correctly, the previous criteria if ($field[16] eq 'Mutation ID' or $field[16] eq 'GENOMIC_MUTATION_ID') no longer works in v91 and v92, because they added a field right before the 17th column (which is $field[16])? If this is the case, I can add a new statement in the code and fix the issue so other users do not need to use the "cut" command. Thank you.

[RKV82]

@RKV82 Thank you, if I understand correctly, the previous criteria if ($field[16] eq 'Mutation ID' or $field[16] eq 'GENOMIC_MUTATION_ID') no longer works in v91 and v92, because they added a field right before the 17th column (which is $field[16])?

@kaichop Yes, the field 16 now is "Genome-wide screen". The field 17 in COSMIC Mutation Data (Genome Screens) is "MUTATION_ID", but for COSMIC Complete Mutation Data (Targeted Screens) and Mutations in Census Genes it named "GENOMIC_MUTATION_ID" On the attached image the top string is from COSMIC Mutation Data (Genome Screens) and the bottom one is from COSMIC Complete Mutation Data (Targeted Screens) Glad to help in your great work!

[kaichop]

The issue was fixed, and the updated script works on all four types of files (CosmicMutantExport.tsv, CosmicCompleteTargetedScreensMutantExport.tsv, CosmicGenomeScreensMutantExport.tsv, CosmicNCV.tsv).