Dear all,

I am looking for a tool that would help me to predict SNV effect.

I work with viral deep sequencing data. Briefly, during the data analysis, I align the reads and call a consensus sequence using CLC genomics. I sort the aligned BAM files with SAMtools and then I call minor variants (SNVs) with iVar v1.0 .

To predict SNP protein effect I use Geneious where I load the consensus sequences and I annotate the SNPs.

I am interested in doing the same with the minor variants (SNVs). The output of the variant calling that I perform using iVar is a tsv file looking like:

POS REF ALT ALT_FREQ

7 A G 0.0784037

10 T A 0.00122362

Basically it tells me for each position (POS) what is the nucleotide in the reference meaning in my consensus sequence (REF) and whether there is a variant, what we call minor variant or not (ALT) and if there is, it outputs its frequency (ALT_FREQ).

Do you know any tool that takes tsv file as input and would predict the proetin effect (syn or non-synonymous) ? Of course, a part from the tsv file an annotated reference genome would be needed, but that I could provide that easily.

Thanks for your help!!