i am trying to annotate of identified SNPs and INDELs (vcf format) using software such as snpEff. i downloaded gff3 file correspond to my reference genome. i have to build database in snpEff because my desired database is not present in snpEff.
problem: scaffold names in gff3 file and VCF file are different and i must to convert scaffold names in gff3 file to scaffolds name in VCF file and then try to building new database in snpEff using name-converted gff3 file. anybody here know how i can do it?
example of differences in scoffold names
name in gff3 * name in VCF
NW_011590949.1 * KN271049.1
NW_011590950.1 * KN271050.1
are there alternative ways to annotate new SNPs? it is possible to merge gff and VCF to annotate VCF file?
thanks in advance