Generating wANNOVAR output with ANNOVAR

Question

[paolo]

I have written an R-script for prioritizing variants which uses a file annotated by wANNOVAR as input.

But since wANNOVAR can not annotate VCF files larger than 50Mb, if I want to use my script for VCFs from WGS, I must find another way to annotate my VCF, while keeping the same columns of the wANNOVAR output.

I have learned to use ANNOVAR and I am now in the process of downloading the databases necessary to obtain a wANNOVAR-like output.

To speed up the process, does anyone know the table_annovar.pl command used for generating the wANNOVAR output with ANNOVAR?

[barslmn]

I don't think there would be tool that does what you're asking for. You would have to preprocess the output yourself.

[paolo]

Yes, exactly. To do so you need to use an ANNOVAR command that will be something like this:

perl table_annovar.pl VCF_files/test.vcf humandb/ -buildver hg19 -out test -remove -protocol ensGene,ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EAS.sites.2015_08,EUR.sites.2015_08,SAS.sites.2015_08,exac03,dbnsfp30a -operation g,f,f,f,f,f,f,f,f -nastring . -vcfinput -polish

But this still lacks several columns of the wANNOVAR output. I am checking one by one these columns and I am downloading the needed databases.

But I wondered if someone add already performed this task.

Answer 1

[paolo]

I have managed to generate the annotation of wANNOVAR by using ANNOVAR even though I have not been able to find the database containing data from the GWAS catalog (p values, beta, ORs...)