Running and Verifying SnpEff

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to list the databases (genomes) supported by SnpEff:

   java -jar snpEff.jar databases

3. Run the following command to switch to the SnpEff directory:

   cd /path/to/SNPEFF/snpEff

4. Run the following command to export the text that includes comments:

   java -jar snpEff.jar -v GRCh37.75 /path/to/SNPEFF/snpEff/examples/test.chr22.vcf  >  test.chr22.out.vcf

   After the execution is complete, three files are generated: snpEff_genes.txt, snpEff_summary.html, and test.chr22.out.vcf.

   The following is an output example: