Annapotater

A quick and dirty SNP annotator. Only annotates SYNONYMOUS, NONSYNONYMOUS, STOP, STOPLOST, or NA. NA stands for "not assessed."

Does not work on multisnp sites or indels.

Installation

Step 1: download the latest release and decompress it somewhere, e.g., $HOME/bin/.../ and then cd into the annapotater folder.

cd annapotater
perl Makefile.PL
cpanm --installdeps .
make
make test
# Make install is optional, if you want to put the script in $HOME/bin
make install

Usage

annapotater.pl t/data/MN908947.3.gbk t/data/SRR12894848.vcf.gz

Give it a genbank file with CDS features and sequence, and the next parameter is a gzipped VCF file. Use --prot to include protein translations. Use --all to output all sites, useful as a passthrough.

Output

Prints vcf to stdout. Only prints sites that are annotated.

Adds a notation onto the INFO field with the key EFF. E.g., EFF=NONSYNONYMOUS

If you give --prot, will also have a field AA=.

Requirements

• perl and perl modules:
  • BioPerl
  • Array::IntSpan

Etymology

Sounds like "annotator" but:
Tomato, tomato
Potato, potato
Anna, anna

And also, in some places, 'tater' is slang for 'potato.'