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from genome position to protein position

Hello,

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,

protein snp genome bacteria position
• 2,067 views • link
written by vujex • vujex

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

• 0 views • link
written by cpad0112 cpad0112

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...

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written by vujex • vujex

is it annotated?

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written by cpad0112 cpad0112

it is annotated

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written by vujex • vujex

can you share the link for downloading annotated file?

• 0 views • link
written by cpad0112 cpad0112

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