Annovar is installed on fourierseq at /opt/annovar. Annovar is a useful tool for functional annotation of SNPs. It will annotate whether the snp is known/novel, whether it is an exonic region or otherwise, the amino acid changes it would cause and scores to determine the damage potential of the snp.
To generate a summary annovar report on your SNPs, using Human hg19 genome, follow the steps below:
1. Convert vcf snp file to annovar format
convert2annovar.pl -format vcf4 --inlcudeinfo out.vcf > out.vcf.annovar