prepare new cosmic data

[asmlgkj]

Dear professor, Thanks a lot for making such a great tool. if I want to do a cosmic file of version94

For COSMIC v91, v92 and beyond, the file formats are changed slightly. In Oct 2020 the prepare_annovar_user.pl is slightly modified to handle the new file formats:

prepare_annovar_user.pl -dbtype cosmic CosmicMutantExport.tsv -vcf CosmicCodingMuts.normal.vcf > hg19_cosmic94_coding.txt prepare_annovar_user.pl -dbtype cosmic CosmicNCV.tsv -vcf CosmicNonCodingVariants.normal.vcf > hg19_cosmic94_noncoding.txt

but command always like this

-protocol refGeneWithVer,1000g2015aug_all,clinvar_20211002,avsnp150,cosmic94, here generate 2 files hg19_cosmic94_coding.txt hg19_cosmic94_noncoding.txt, how should I write the command.

if I follow the earlier command Use this command prepare_annovar_user.pl -dbtype cosmic CosmicMutantExport.tsv -vcf CosmicCodingMuts.vcf > hg19_cosmic94.txt
does this not normalize the variant and will cause mismatch? <> and I found the hg19_cosmic94_coding.txt is much like hg19_cosmic94.txt,

[YeHW]

Hi asmlgkj,

-protocol refGeneWithVer,1000g2015aug_all,clinvar_20211002,avsnp150,cosmic94_coding,cosmic94_noncoding should work.