Annovar using VCF file

Question

[Samar]

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 multi-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

[Sam]

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
#___________________________________________________________________________________________________^^^^

Answer 1

[manuel.belmadani]

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.