exoclasma-note

Annotation of genomic variants.

Dependencies

Perl:

sudo apt install perl

Annovar:

GENOME="hg19" # hg38 if you prefer
curl --output annovar.latest.tar.gz www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
tar -xzf annovar.latest.tar.gz
cd annovar
for database in refGene knownGene ensGene dbnsfp35c dbscsnv11 intervar_20180118 gnomad211_genome gene4denovo201907 kaviar_20150923 hrcr1 abraom 1000g2015aug gme esp6500siv2_all avsnp150 clinvar_20200316 regsnpintron revel gwava;
do {
	perl annotate_variation.pl -downdb -buildver ${GENOME} -webfrom annovar ${database} humandb/
} done
cd ..
rm annovar.latest.tar.gz

Install

sudo python3 -m pip install exoclasma-note

Usage

exoclasma-note -u ${unit_json} -a ${annovar_folder} -g ${genome} [--nofilter]

• unit_json: Unit JSON file which was created by exoclasma-pipe
• annovar_folder: Path to ANNOVAR folder where perl scripts are located
• genome: Genome assembly which use ANNOVAR (i.e., hg19, hg38, etc.)