1. Go to the website http://snpeff.sourceforge.net/ and download snpeff:
wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip
2. Unzip and install
unzip snpEff_latest_core.zip
After decompression, the following picture appears:
3. Annotation variation:
/path/to/java -Xmx4g -jar snpEff.jar GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf #test.chr22.vcf refers to the input file containing variants, test.chr22. ann.vcf refers to the annotation output file containing variants
Note: Since snpeff is a java-based software package, it needs to be run in an environment with java, so install java before using this toolkit. If java has been installed, ignore this.
The result file is as follows:
Reference link: http://snpeff.sourceforge.net/