Hello everyone. I want to annotate my vcf file and transfer it to tabular, so I can count the gene that content mutation maximum in number. When I use ANNOVAR Annotate VCF to annotate my vcf file, I cannot choose the annotation file downloaded from NCBI in my history, and there is no option in the database. I want to know how do I deal with this error or if there are other possible tools to get the same result. My workflow is as following.
This is my workflow
Hi @Abieskawa,
ANNOVAR is currently not functional; I suggest you to use SnpEff for performing such analysis. The generated VCF file can be easily converted to tabular by using the VCFtoTab tool, and by using a simple regular expression you can extract the gene names.
You can find some information about how to use SnpEff in the following entry.
Regards