VCF problem

[szyszka]

I obtained a vcf file from mutect that is structured like this and is not accepted by any annotation tools like Ingenuity Variariant Analysis, etc. Can anyone please advice me on what is the problem and how can it be solved?

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 52
1 1225522 . T C . PASS SOMATIC;VT=SNP GT:AD:BQ: DP:FA:SS 0:67,2:.:68:0.029:0
1 2372079 . G A . PASS SOMATIC;VT=SNP GT:AD:BQ: DP:FA:SS 0:9,0:.:8:0.00:0
1 21806315 rs61775949 G C . PASS DB;SOMATIC;VT=SNP GT:AD:BQ: DP:FA:SS 0:21,0:.:21:0.00:0
1 35649701 . G T . PASS SOMATIC;VT=SNP GT:AD:BQ: DP:FA:SS 0:44,0:.:44:0.00:0

[sophiespo]

Just a guess but is the program expecting a tabbed VCF file?
I have had problems when I've had spaces rather than tabs between fields.

[vivek_]

Even a minimal VCF file needs to have the fileformat information in the header:

##fileformat=VCFv4.0

Also it would be helpful if you can reproduce an error from the tools you have used.