Question: Annovar VCF annotation syntax error
1
gravatar for er.doug.ragnar
19 months 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 • 748 views
ADD COMMENTlink modified 19 months ago by Kevin Blighe50k • written 19 months ago by er.doug.ragnar20
0
gravatar for Kevin Blighe
19 months ago by
Kevin Blighe50k
Kevin Blighe50k 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 19 months ago by Kevin Blighe50k

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 19 months 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 19 months ago by er.doug.ragnar20

Hello, glad that you got it sorted out!

ADD REPLYlink written 19 months ago by Kevin Blighe50k
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