Modifying Annovar Command Line: table_annovar.pl

Question

[ghalib.bardai]

Hello, I have been using the table_annovar.pl successfully to annotate variants. However, my programming skills are non-existent and I require some help.

Here is the command line I use successfully:

$ perl table_annovar.pl example/3149_v1.vcf humandb/ -buildver hg19 -out 3149 -remove -protocol refGene,cytoBand,exac03,esp6500siv2_aa,1000g2015aug_all,snp138,dbnsfp30a,clinvar_20160302,ljb26_all,dbscsnv11 -operation g,r,f,f,f,f,f,f,f,f -nastring . -vcfinput

What I want to do is the following as described on the Annovar website:

The -arg argument is now supported, so that you can supply a list of comma-delimited optional arguments to table_annovar for each of the annotation tasks. For example, adding -arg '-splicing 5',,,,,,,,,,,, to the command will add change the splicing threshold to 5bp for the gene-based annotation. The use of -arg argument allows one to fully realize the potential of table_annovar to suit user needs in a much more customized manner.

My Question is: How do I modify the command line I use successfully to do what is described above.

Thank you very much for any help you can provide. Ghalib

[Zaag]

My guess is you just add this to your command:

-arg '-splicing 5'

and if you want to add other things seperate them with a comma:

 -arg '-splicing 5', '-some_other_setting VALUE'