Hi everyone! I am looking for some suggestions how can I annotate a VCF file without having the GTF/GFF for my reference genome. The VCF file created from a custom reference genome (de novo assembly) for Reticulitermes flavipes, therefore there are no annotations available. I want to annotate the VCF in order to later find # of variants (SNPs) per gene.
Hi @jradfor8,
one of the possibilities is to use vcf-annotator. Despite this tool is not actually in Galaxy, it can be included if you consider it adequate.
Regards.