bushlab/snpeff repository overview

This is a container for running SnpEff v5.1d.

⁠Running the container

Run the container in interactive mode with the following command:

docker run -it bushlab/snpeff:latest

SnpEff has been installed at /snpEff within the container.

⁠Running SnpEff on Example Files

SnpEff can be tested by running

java -Xmx8g -jar snpEff.jar GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf

This will create an annotated file called test.chr22.ann.vcf.

⁠References

SnpEff documentation can be found here.⁠

"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672