I am working on some environmental data, a metagenomic dataset that come from the Arctic ocean during winter.
Among this dataset I have extracted all sequences that belong to Bathycoccus prasinos and I have aligned them against the reference genome of this algae and then cretaed a vcf file.
Now, I am trying to annotate all the variant contined in this vcf file. I tried using snpEff, but I was wondering if anyone of you will know what software is more suitable for non human data? If anyone has an idea of what tool to use (and if possible why) for annotating variant for marine protist species it would be really cool :)
and have a good day.