Does anyone know a tool to go from genomic positions to protein and to see whether SNPs are (non)synonymous in bacteria?
Doing it manually in IGV would take too much time...
I have experience with Python, R and bash.
Thanks in advance,
Convert SNPs into text file that VEP can accept (or VCF) and assuming that mentioned bacterial genomes are sequenced and annotated, VEP will furnish syn, non-syn annotations of input SNPs
Thanks, the problem is that my bacterial genome is not on ensembl - I don't see a way to use VEP with a new genome...
is it annotated?
it is annotated
can you share the link for downloading annotated file?
It is this one H37Rv reference genome of Mtb: https://www.ncbi.nlm.nih.gov/assembly/GCF_000195955.2
For some reason it seems to have disappeared from ensembl....
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