I am newbie to NGS
I have mapped my illumina reads to non-model assembled reference contigs. By variant calling I have VCF format with SNPs predicted per contig. I dont have any information on chromosome location, intron exon boundary position. I want to calculate synonymous nonsynonymous ratio. I think I should go for contig SNP annotation starting with blast with other model species, then try to find intron exon boundaries using gene prediction programme like Genscan and then I can calculate synonymous nonsynonymous ratio using SNPeff. Any suggestion for good workflow?