Annovar VCF annotation syntax error

Question

[er.doug.ragnar]

Hi , I'm trying to annotate my vcf file using Annovar but I keep getting syntax error, I tried rearranging the argument but I always get syntax error. Am I doing the command wrong do I have to convert it to Annovar input formt?

perl table_annovar.pl --vcfdbfile ./AmH01.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f -nastring . -vcfinput
Syntax error

Answer 1

[Kevin Blighe]

The problem is most likely that you have specified 5 resources for protocol but only 3 for operation. The numbers for each have to match in both number and order.

I think that you need:

-protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f,f,f

[er.doug.ragnar]

Thank you for your answer, I increased the operation resources but I still get Syntax Error

perl table_annovar.pl --vcfdbfile AngH01.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f,f,f -nastring . -csvout -polish -vcfinput Syntax error

[er.doug.ragnar]

I worked out my own error so I will put the correction here for anyone with the same problem:

perl table_annovar.pl --vcfdbfile AngH01.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f,f,f -nastring . -vcfinput

PS. Databases also need to be downloaded correctly otherwise it will also be signaled as an error

[Kevin Blighe]

Hello, glad that you got it sorted out!