I have tried to use SnpEff to annotate the variants identified from two different parasite strains. As suggested, I have first used the SnpEff build to get the database and then SnpEff eff for annotating the variants. Surprisingly, for one parasite strain, the missense-variant for a single nucleotide change (SNP) is correctly annotated, and the amino acid and its position in the reference genome is also correctly indicated, however, the changed amino acid in the newly sequenced strain is not shown with only a question marker, such as L69? see below:
For the second parasite strain genome sequence, all the SNPs are wrongly annotated with frame-shift-variant & missense-variant, as a result, the changed amino acids due to SNP are wrongly annotated as fs though the amino acid and position is correctly annotated for the reference genome.
such as p.Pro903fs see below:
I am wondering what could go wrong and how can it be corrected. Thanks for help.