How to annotate SNPs, identified against scaffolds (draft genome)

Question

[inayat45shaikh]

Hello group, I had identified SNPs by mapping reads to scaffolds (closely related organism) and generated VCF file. The problem I am facing is in annotation. I wanted to classify these variants into exonic, intronic, synonymous, non-synonymous etc. I came across some SNP annotation pipelines I.e. variant effect predictor, SNPeffct, SNPeff SNPsift etc. But the problem working with these pipelines is, they do annotation based on the annotated genomes, available in their achieve. As I am working on the no model eukaryotic organism and had identified SNP against its closely related genome, which is not available in the above annotation pipelines. Is.there other ways to annotate SNPs?

Answer 1

[Sean Davis]

See here for how to build a custom annotation database for snpEff:

http://snpeff.sourceforge.net/SnpEff_manual.html#databases