Snpeff

How to use:

Basic example: Annotate using SnpEff

Let's assume you have a VCF file and you want to annotate the variants in that file. An example file is provided in examples/test.chr22.vcf (this data is from the 1000 Genomes project, so the reference genome is the human genome GRCh37).

You can annotate the file by running the following command (as an input, we use a Variant Call Format (VCF) file available in SnpEff's examples directory).

$ java -Xmx4g -jar snpEff.jar GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf

For a detailed user-guide, please refer to the following URL: http://snpeff.sourceforge.net/SnpEff_manual.html