Hi Dr. Wang,
I use prepare_annovar_user.pl downloaded from http://www.openbioinformatics.org/annovar/download/prepare_annovar_user.pl in order to prepare cosmic v90 dataset for annovar annotation? Back in v90 Cosmic didnt supply a normalised vcf, so that MNVs where given e.g. as followed 17:7577538:CGG/CAA instead of 17:7577539:GG/AA (as displayed in my normalized vcf). I am wondering if you corrected for this in the script from 2018-07-08 to ensure that MNVs get correctly annotated with Cosmic data?
Hi Dr. Wang, I use prepare_annovar_user.pl downloaded from http://www.openbioinformatics.org/annovar/download/prepare_annovar_user.pl in order to prepare cosmic v90 dataset for annovar annotation? Back in v90 Cosmic didnt supply a normalised vcf, so that MNVs where given e.g. as followed 17:7577538:CGG/CAA instead of 17:7577539:GG/AA (as displayed in my normalized vcf). I am wondering if you corrected for this in the script from 2018-07-08 to ensure that MNVs get correctly annotated with Cosmic data?
Thanks a lot.
All the best, Rose
prepare_annovar_user.pl version used: our $REVISION = '$Revision: fcb810b8464da61f2ecb40d529b9fafcdfa13742 $'; our $DATE = '$Date: 2018-07-08 23:15:35 -0400 (Sun, 8 Jul 2018) $';