alexcoppe/snpeff repository overview

⁠Dockerized SnpEff⁠

⁠Usage:

⁠Docker Pull Command:

docker pull alexcoppe/snpeff

⁠Example:

⁠Using SnpEff default command ('eff') to annotate variants in a VCF.

The SnpEff configuratione file (snpEff.config), the genomic data (GRCh37.75) and the VCF are in a Docker engine’s host directory mounted into the container using the -v flag.

docker run --rm -it -v $(pwd):/data  alexcoppe/snpeff eff -v  -c /data/snpEff.config GRCh37.75 /data/sample.vcf