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
- Perl: https://www.perl.org
- BioPerl: https://bioperl.org
- Bio::DB::Fasta
- Bio::SeqIO
- EMBOSS: http://emboss.sourceforge.net or EMBOSS-6.6.0.reduced.tar.gz
- needle
- stretcher
- 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
-
Prepare annotation table file
- Execute Annomen_table.hg38.sh
./Annomen_table.hg38.sh
- Execute Annomen_table.hg38.sh
-
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
- Execute Annomen.hg38.sh