Question: Annovar VCF annotation syntax error
1
gravatar for er.doug.ragnar
2.0 years ago by
er.doug.ragnar20 wrote:

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
annovar vcf • 987 views
ADD COMMENTlink modified 2.0 years ago by Kevin Blighe56k • written 2.0 years ago by er.doug.ragnar20
0
gravatar for Kevin Blighe
2.0 years ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

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
ADD COMMENTlink written 2.0 years ago by Kevin Blighe56k

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

ADD REPLYlink written 2.0 years ago by er.doug.ragnar20
1

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

ADD REPLYlink written 2.0 years ago by er.doug.ragnar20

Hello, glad that you got it sorted out!

ADD REPLYlink written 2.0 years ago by Kevin Blighe56k
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