jiwoongbio / Annomen

Annotate variant nomenclature

Annomen

Annotate variant nomenclature

Annotations

• Gene name
• Region type
  • CDS
  • utr5
  • utr3
  • intron
  • non_coding_exon
  • non_coding_intron
• Mutation class
  • silent
  • missense
  • inframe
  • frameshift
  • nonsense
  • readthrough
  • startcodon
  • splicing
  • junction
• Strand
• Splice distance
• Transcript ID
• Protein ID
• Transcript variation nomenclature
• Protein variation nomenclature

Requirements

1. Perl: https://www.perl.org
2. BioPerl: https://bioperl.org
   • Bio::DB::Fasta
   • Bio::SeqIO
3. EMBOSS: http://emboss.sourceforge.net or EMBOSS-6.6.0.reduced.tar.gz
   • needle
   • stretcher
4. Basic linux commands: bash, rm, gzip, sort, echo, find, sed, awk, wget

You can use conda to install the requirements as follows:

conda create -n Annomen -c bioconda perl perl-bioperl emboss
conda install -n Annomen -c anaconda wget

Install

If you already have Git (https://git-scm.com) installed, you can get the latest development version using Git.

git clone https://github.com/jiwoongbio/Annomen.git

Usages

1. Prepare annotation table file

   • Execute Annomen_table.hg38.sh

     ./Annomen_table.hg38.sh
     

2. Annotate variant file in VCF or tab-separated columns of chromosome, position, reference base, variant base

   • Execute Annomen.hg38.sh

     ./Annomen.hg38.sh <input file>
     

   • Example: annotating ClinVar variants

     ./clinvar.sh