Question: Annovar using VCF file
0
gravatar for Samar
3.5 years ago by
Samar0
India
Samar0 wrote:

Hi all, I have a VCF file that I want to annotate using Annovar. I tried using convert2annovar.pl command but since I have a milti-sample file, it generates separate avinput files. I want one single file with all the sample information.

So I now used the command:

table_annovar.pl /archive/samarpana/2_Unified_Genotyper/Family2/Family2.vcf humandb/ -buildver hg19 myanno -remove -protocol refGene,phastConsElements46way,esp6500siv2_all,1000g2015aug_all,avsnp144,exac03,ljb26_all,avsift -operation g,r,f,f,f,f,f,f -nastring . -csvout

and also, 

table_annovar.pl /archive/samarpana/2_Unified_Genotyper/Family2/Family2.vcf humandb/ -buildver hg19 myanno -remove -protocol refGene,phastConsElements46way,esp6500siv2_all,1000g2015aug_all,avsnp144,exac03,ljb26_all,avsift -operation g,r,f,f,f,f,f,f -nastring NA -vcfinput

 

But none of the commands are working. I am getting error message saying Syntax error. Can anyone suggest what I am doing wrong?

 

Thanks

 

ADD COMMENTlink modified 3.2 years ago by poojayakshi10 • written 3.5 years ago by Samar0

Can you try

table_annovar.pl /archive/samarpana/2_Unified_Genotyper/Family2/Family2.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,phastConsElements46way,esp6500siv2_all,1000g2015aug_all,avsnp144,exac03,ljb26_all,avsift -operation g,r,f,f,f,f,f,f -nastring NA -vcfinput
ADD REPLYlink written 3.5 years ago by Sam2.3k
1
gravatar for manuel.belmadani
3.2 years ago by
Canada
manuel.belmadani730 wrote:

As @Sam pointed out, you're missing the  -out before myanno. The -vcfinput argument (which you had in the second command but not your first) is also necessary, and omitting it wouldn't cause the "Syntax error" message, but instead all your variants would get discarded (and written to myanno.invalid_input )

I think your main problem is that Annovar complains when -nastring is not '.' when using -vcfinput . This will give you an Syntax Error message like you described.

table_annovar.pl /archive/samarpana/2_Unified_Genotyper/Family2/Family2.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,phastConsElements46way,esp6500siv2_all,1000g2015aug_all,avsnp144,exac03,ljb26_all,avsift -operation g,r,f,f,f,f,f,f -nastring . -vcfinput

The above line should work.

 

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by manuel.belmadani730
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