Web page:

Registered from with the following information,

User Name:
User Email:
User Institution: University of Cambridge

then copy the link received from email and issue commands from csd3,

cd ${HPC_WORK}
tar xvfz annovar.latest.tar.gz
ls *pl | sed 's/*//g' | parallel -C' ' 'ln -sf ${HPC_WORK}/annovar/{} ${HPC_WORK}/bin/{}'

Additionally, one can download the ENSEMBL genes and whole-genome FASTA files to humandb/hg19_seq for CCDS/GENCODE annotation.

cd annovar
# ENSEMBL genes -buildver hg19 -downdb -webfrom annovar ensGene -build hg19 -out ex1 -dbtype ensGene example/ex1.avinput humandb/
# reference genome in FASTA -downdb -build hg19 seq humandb/hg19_seq/
# CCDS genes -downdb -build hg19 ccdsGene humandb humandb/hg19_ccdsGene.txt -seqdir humandb/hg19_seq -format refGene \
                           -outfile humandb/hg19_ccdsGeneMrna.fa -build hg19 -out ex1 -dbtype ccdsGene example/ex1.avinput humandb/
# GENCODE genes -downdb wgEncodeGencodeBasicV19 humandb/ -build hg19 -format genericGene -seqdir humandb/hg19_seq/ \
                           -outfile humandb/hg19_wgEncodeGencodeBasicV19Mrna.fa humandb/hg19_wgEncodeGencodeBasicV19.txt -build hg19 -out ex1 -dbtype wgEncodeGencodeBasicV19 example/ex1.avinput humandb/

We can have region-based annotation as in,

# Conserved genomic elements -build hg19 -downdb phastConsElements46way humandb/ -regionanno -build hg19 -out ex1 -dbtype phastConsElements46way example/ex1.avinput humandb/ -regionanno -build hg19 -out ex1 -dbtype phastConsElements46way example/ex1.avinput humandb/ -normscore_threshold 400
# Transcription factor binding sites -build hg19 -downdb tfbsConsSites humandb/ -regionanno -build hg19 -out ex1 -dbtype tfbsConsSites example/ex1.avinput humandb/
# Cytogenetic band -build hg19 -downdb cytoBand humandb/ -regionanno -build hg19 -out ex1 -dbtype cytoBand example/ex1.avinput humandb/
# microRNA, snoRNA -build hg19 -downdb wgRna humandb/ -regionanno -build hg19 -out ex1 -dbtype wgRna example/ex1.avinput humandb/
# previously reported structural variants -build hg19 -downdb dgvMerged humandb/ -regionanno -build hg19 -out ex1 -dbtype dgvMerged example/ex1.avinput humandb/
# published GWAS -build hg19 -downdb gwasCatalog humandb/ -regionanno -build hg19 -out ex1 -dbtype gwasCatalog example/ex1.avinput humandb/

Here is a more sophisticated example contrasting with,

if [ ! -d test ]; then mkdir test; fi -buildver hg19 -downdb -webfrom annovar refGene test/ -buildver hg19 -downdb -webfrom annovar exac03 test/ -buildver hg19 -downdb -webfrom annovar avsnp147 test/ -buildver hg19 -downdb -webfrom annovar dbnsfp30a test/ -geneanno -dbtype refGene -buildver hg19 example/ex1.avinput test/ -filter -dbtype exac03 -buildver hg19 example/ex1.avinput test/ example/ex1.avinput test/ -buildver hg19 -out myanno \
     -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a,gwasCatalog -operation g,r,f,f,f,r \
     -nastring . -csvout -polish -xref example/gene_xref.txt example/ex1.avinput test/ -buildver hg19 --outfile ex1 \
     -protocol ensGene,refGene,ccdsGene,wgEncodeGencodeBasicV19,cytoBand,exac03,avsnp147,dbnsfp30a,gwasCatalog \
     -operation g,g,g,g,r,f,f,f,r \
     -csvout -polish -remove -nastring .

The second above works after symbolic links to relevant databases at humandb/ were created at test/.

It is handy to create a VCF file to be used by VEP (see below), -format annovar2vcf example/ex1.avinput > ex1.vcf
vep -i ex1.vcf -o ex1.vcfoutput --offline --force_overwrite