👶How to run Annovar for SNV annotation

As including all Annovar dependency datasets would make SUMMER docker image taking too much memory, here we list how to use Annovar from de novo.

Guidance for Annovar downloading is also detailed at: https://annovar.openbioinformatics.org/en/latest/user-guide/download/

Please firstly fill your personal information at https://www.openbioinformatics.org/annovar/annovar_download_form.php to download the latest version.

The software would then be sent to your email.

#download Annovar and unzip according to the link sent to your email
wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz 
tar -zxvf annovar.latest.tar 
cd annovar

See user guide at : https://annovar.openbioinformatics.org/en/latest/user-guide/startup/

General usage see https://annovar.openbioinformatics.org/en/latest/user-guide/gene/#command-overview for details.

And here's a quick example to download database:

perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/
perl annotate_variation.pl -downdb -buildver hg38 -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGeneWithVer humandb/ 
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGeneWithVer humandb/
perl annotate_variation.pl -buildver hg19 -downdb cytoBand humandb/
perl annotate_variation.pl -buildver hg38 -downdb cytoBand humandb/
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar gnomad211_exome humandb/ 
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad211_exome humandb/ 
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp151 humandb/ 
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp151 humandb/ 
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp47a humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp47a humandb/

Additional database available list at: https://annovar.openbioinformatics.org/en/latest/user-guide/download/#additional-databases

#Simplest example:
perl annotate_variation.pl -out ex1 -build hg19 example/ex1.avinput humandb/

#Another example:

perl table_annovar.pl example/ex1.avinput \
  humandb/ \
  -buildver hg19 \
  -out ex1_anno \
  -protocol refGeneWithVer,cytoBand,gnomad211_exome,avsnp151,dbnsfp47a \
  -operation gx,r,f,f,f \
  -xref example/gene_xref.txt \
  -remove -nastring . -csvout -polish

#A true example:
perl convert2annovar.pl -format vcf4  /lustre/home/2311110279/merge_output.vcf -outfile ./output  -allsample -withfreq -include
perl table_annovar.pl /lustre/home/2311110279/software/annovar/output \
  humandb/ \
  -buildver hg38 \
  -out output.out \
  -protocol refGeneWithVer,cytoBand,gnomad211_exome,avsnp151,dbnsfp47a \
  -operation gx,r,f,f,f \
  -xref example/gene_xref.txt \
  -remove -nastring . -csvout -polish

#sample format

perl convert2annovar.pl -format vcf4  {workdir/sample.vcf} -outfile {workdir/sample}  -allsample -withfreq -include
perl table_annovar.pl {workdir/sample} \
  humandb/ \
  -buildver hg38 \
  -out {outdir/outfile} \
  -protocol refGeneWithVer,cytoBand,gnomad211_exome,avsnp151,dbnsfp47a \
  -operation gx,r,f,f,f \
  -xref example/gene_xref.txt \
  -remove -nastring . -csvout -polish